I like the cast as listed in the first pic in this thread the most (like the idea of teams, as oppose to just one person).
I like the idea that there is a bounty on your head (and you know it), including your last known whereabouts and all the hunters are coming to collect. They are all competing bounty hunters (with the pictured character as leader), so possible alliances/competition/ignoring/killing off as would be appropriate. They don't necessarily know the others are after you. It is hosted in the universe of the defender and the hunters can bring what they want of their resources from their own universes, and are able to get whatever they could reasonably obtain from the host universe.
Darth Vader and the Star Destroyer - I am addressing first because he has been most popular. And I totally disagree.
Movie Version
The storm troopers are entirely useless, Vader only really uses choke and is a fairly awful sword fighter. Seriously, give me a lightsaber and choke immunity and I'd beat him in a sword fight.
Extended
First up, he is still powerful as Vader, but you can ignore everything he does as Anakin in Clone Wars. According to Lore he loses much of his power when becoming Vader, both from the extensive injuries and cybernetic replacements (only living creatures can use the force) and because he never fully mentally recovers from what happened to him.
Force - The problem here is that you and all the other contestants would very likely be completely force immune. No magic lizard required. You'd be undetectable and immune to direct usage (indirect would be fine). In short, you'd be
Yuuzhan Vong. They are the only extra-galactic organic race and they are only connected to the force while they have their sentient home planet (which may be from within the Galaxy). Once they lose that, they are outside the force and untouchable by it as listed. Given how far, far away our galaxy is supposed to be, I'd say it's likely we'd be the same.
Next up, Vader still only really uses chokes and general pushes etc. He very rarely uses lightning because of his suit (more on that later). Also, we'd be immune to lightning as are the Yuuzhan. So he'd be able to throw stuff at you and augment his strength a bit.
Lightsaber - Cuts through a lot of stuff, but not everything. There are many things that can resist it. SIth Alchemy can make other materials lightsaber resistant for example. Most notably though; Mandalorian Iron, which can withstand it very well. And it withstands it entirely by being an amazingly tough metal alloy.
Vader can only block stuff with it as fast as he can move to intercept it. He can see attacks coming just before they happen, but he still has to get the sword in the way, and this can be beaten, otherwise no force user would ever lose a swordfight. Standard operating procedure for dealing with force users is overwhelming firepower (Ala Silencer's suggestion of very fast firing weapons, or lots of weapons firing) or using things sabers can't block, such as flamethrowers. He is at least meant to be a very good, but limited saber fighter. He mostly wins fights through sheer offensive power, aided by extra strength from bionic limbs. He lacks some speed and is fairly...stiff (nimble opponents have been known to dance around him quite well). Maybe not pertinent, but his lightsaber instantly fails if submerged in water (most do unless especially modified to not).
Suit/Armour - This is where Vader's real kryptonite comes in (the force nulling thing is just a weakening, kryptonite actually hurts Superman, not just weakens him). You see, the suit is also his life support system. If it breaks, he dies slowly. And while dying only has the use of one limb (all his others are mechanical and controlled/powered by the suit) and the suit is VERY susceptible to electricity. This is why he very rarely uses force lightning, it may kill him. This is why the Emperor's lightning kills him, it breaks the suit. So anyone who thinks to use an EMP blast or electrical attack on the guy very clearly wearing electronics will kill him with something neither the force, nor his lightsaber can protect him from. Also, if even his mask is off, he will slowly die. His mask does allow him infrared and nightvision and tactical overlays for piloting. His armour affords him a small amount of protection, but it is very little. He specifically keeps it this way so as not to become dependent on it for his defence.
Death Star - I am going with Death Star v1, because that's the only one that gets finished. So no Emperor, which fits the "story" because he wouldn't do as Vader says anyway. It has it's obvious weakness, but luckily most others wouldn't know it. However that weakness suggests the core is very unstable, so still susceptible to sabotage. He would have a hell of a lot of storm troopers at his disposal. Storm troopers would be effective, but not awfully so. While the movie depiction isn't how they're shown in the EU, it is still canon that they lost to the ewoks. They're probably better shots, but still a bad army on the whole. Still, sheer numbers plus fleets of ships and planet destroying power is a plus. It also has bad central control and elements are very hackable (as R2D2 often shows).
Predator Elite - Probably my bet as defenders (their defender universe would be the AvP comics one, so humans have interplanetary flight, but it's not fantastic)
First thing to keep in mind, they hunt for honour, but they do know how to and are willing to put the hunt aside when necessary, they are very pragmatic when required. As a hunter, they'd probably stick to it where possible, as protector, they would ignore it excluding the occasional indulgence (this is a big part of why I think they'd win as a protector)
Elites - These guys are an actual caste, and they are tough. Seriously, to become an elite you have to have killed a xenomorph queen in a hunt. These are all veteran hunters and warriors that are most likely hundreds of years old. They have their own ships, and can access all weapons and equipment their species has (younger less experienced predators are limited in which weapons they're allowed to use). They are also allowed to seed xenomorphs for hunting.
Stealth - A few of you have gotten this wrong. Their stealth cannot be seen through with infrared, it bends more than visible light. In the AvP games the only way to see a stealthed predator with another predator, is tech vision, which analyses EMF. It's not visible via heat vision. This means it is not visible to Vader's mask. It can still be seen through, as it isn't quite perfect, but this mostly only happens when seeing them move. Is the sort of flaw other experienced hunters like Wolverine have a good chance at noticing on a predator. But in the vastness of space, their ships might as well be completely invisible.
Weapons - They do have a lot of martial weapons, and the Elites are VERY good with them (most will specialise with a weapon). However they have a variety of different weapons too. Their slicey nets, the homing discs and of course their plasma casters. There are also handheld versions of the plasma casters. Lastly, do no underestimate the usefulness of a nuclear hara-kiri. They do not have the sort of weapons that would be very good at getting through Vader in an honour fight, but Vader is unlikely to survive killing the first one (especially noting that he cannot run). And finally, they have bombs and ship mounted weapons capable of wiping countries out of existence (most often used for destroying out of control xenomorph infestations). They wouldn't use these as a hunter, but if charged with protecting you, they'd use them against a Death Star coming after you.
Physically - They would probably be a match for Vader's strength as they've been shown to be able to break concrete (and they're about the same height which is nice). They are also surprisingly hard to kill and fairly quick healers (by ordinary standards, not x-gene healing factor kind of fast)
Xenomorphs - Seeding them would be very effective against every other large force listed, except Skynet. I also imagine the Judges being pretty good against them. Their vigilance, ruthlessness and telepath/s would possibly stop them being able to take hold. I said "large force", so that's not including X-Men, Gotham's Finest and Hellboy Crew. Probably not bad against Gotham team, provided it isn't Batman himself that finds the eggs first. I have a great mental image of a chestburster trying to get out of Wolverines chest

Would be hilarious to seed onto the Death Star, I want to see a movie of that

So yeah, some running and hiding you while the others take out those hunting you would be pretty effective.
Wolverine and the X-Men
Phoenix is not included, she is not an X-Man and would not follow Wolverine. There is still a pretty friggin' solid roster if you're looking at most of the school though.
Hunters - As hunter's I'd probably look at something akin to the usual team from the original cartoon: Cyclops, Storm, Rogue, Jean, Nightcrawler. Add in a few regulars from comic teams: Shadowcat, Colossus. There are plenty of others, but they'd make an excellent hunter team. Jean can get information from people on your whereabouts, spot traps and semi-nullify stealthed enemies. As well as few others having a way to combat mind attacks. Nightcrawler and Shadowcat can bypass a lot of security and easily close with enemies more suited for ranged fighting. Storm and Cyclops are always useful in a fight.
Wolverine and/or Colossus versus Darth Vader. The question of toughness. This is why I mentioned Mandalorian Iron earlier. It is a metal alloy in the Star Wars universe that can withstand lightsabers purely from toughness, no Sith alchemy required. If Mandalorian Iron can, I argue that Adamantium definitely can and Colossus most likely can. This means both Wolverine'ss claws and HIS ENTIRE SKELETON are effectively lightsaber proof. The rest of him could still be hurt, but the surprise at Vader'ss first solid killing strike failing would probably be enough for Wolverine to kill him (Vader's arrogance in duels he thinks he outclasses the enemy is a noted weakness of his). If it wasn't enough, they both have similar combat styles (very agressive and overpowering), and Wolverine is also a master swordsman, I could see either winning. If Colossus can withstand it, he has Vader pretty solidly beat. He's at least as strong and would be impervious to pretty much any damage done to him in a duel with Vader.
Defenders - As defenders you could hide at the school, giving you a huge number of powerful protectors. The main problem I see is the Death Star planet destruction. Though, if they knew it was coming (between Xavier and Cerebro there's a good chance), they would actually have a chance for defence. This defence would actually come in terms of their home field advantage. That being; neither Scarlet Witch nor Magneto would approve of their planet being blown up, and both would have the power to do something about it. That is borderline cheating, but I'd allow it.
Oh, Dr Strange would probably have something to say about blowing up Earth too
Marv and Company
Pff, yeah right.
Hellboy and Crew
This is the group I think I can do the least justice to, unfortunately. I don't know them beyond the movies and it is currently a bit too late for me to research him properly.
The main two things I'll say is that I'd argue his stone hand is lightsaber proof/resistant as it is magically reinforced (and sith alchemy can magically make armour lightsaber resistant). For fairness I'd say it would withstand pretty much anything thrown at it, even if the rest of him isn't as resilient (it's the right arm of the being that created earth after all). Also, as hunters, him and Liz Sherman would make a fairly hard to stop pair even without the rest of the team. Him being able to pummel you while she smothers the entire room in fire (which he is entirely immune to) is hard to counter.
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Oh shit... Hahahaha! Hellboy in his entirety would be completely immune to lightsabers and all laser/plasma weapons! He is completely immune to all heat based damage. This even extends to being unharmed by electricity (because it damages by burning). This certainly increases his his chances and effectiveness against the Star Wars and Predator teams. I'm not sure he has much defence against planet destruction though...
Also, I will refer people to someone on the first page mentioning him letting you die, then bringing you back when the hunters are gone. If he can do that then that strategy cannot be underestimated as a "defence".
Gotham's Finest - Note "Gotham's" not "DC's", so no Superman in the team. In part because Superman is stoopid.
Hunters - They'd have a chance, but they'd probably be one of the last to get to you. Given they'd do extensive recon and threat assessment of the universe they're now in. They'd have a great chance against any basic earth based protector (Skynet, Judges, Robocop), but I dunno beyond that. I can't see them getting through Xavier's School on high alert. Yes, yes, master planner mcguffin extraordinaire. But he wouldn't be able to carry enough Achilles heel devices to get through the variety of abilities the school holds. And none of his allies are superpowered. They'd do well in the Star Wars universe I think, and he would be able to get an EMP device to neutralise Vader. I don't think he could take on a Predator elite in a one on one fight (he is not unbeatable in a fight, in every good mythos Bane breaks his back)(but his team could take out one at a time together), he couldn't track you down in their universe very well. I don't know how well he'd fair vs Hellboy Crew. Partly limited knowledge, but also, Hellboy has no Achilles heel, and there would probably be scant information about him and his team around for Batman to get anyway (unless it's after the second movie I suppose).
Defenders - I... don't think they'd have a lot of chance. Few in number vs forces like Skynet... Judge's and X-Men telepath nulls a lot of traps. If Vader doesn't try and blow up the planet (thereby incurring the wrath of Superman...I let the X-Men do it...Although there is much less chance DC universe would see it coming) then he'd have a good chance on sheer numbers provided he doesn't lead the assault and get EMP'd to death. Basically, Batman's forte is in being the hunter, he doesn't have much to combat armies coming after him.
Skynet/Judges/Robocop - Together because they have similar limitations.
Defenders - First and foremost, there is sweet fuck all they can do against the Death Star planet destruction. Barring that, they all basically have small or bigger armies at their disposal. Pretty much limited to fairly modern like tech, but do not underestimate the stuff we can do. They'd have a good chance defending you against Gotham, each other, the Predators (given they'd be using Hunt rules), Hellboy Crew (I think) and possibly X-Men. X-Men's versatility would really come into play (Colossus would be hard to stop and Shadowkat is hard to do anything against).
Hunters - They'd all have a pretty good chance against most. Things like large railguns (which shoot a projectile so fast that the friction ignites the air they fly through and when they hit something they fuck it up in ways physics barely understands) and drones that can shoot 5000 5mm grenades per minute with perfect accuracy are rather hard to stop.
Judges - Notable bonus ability, they can have telepaths. Telepaths of the "I can sense you through walls on the fly" and "I can sense your fears and fuck with your head so much I leave you a weeping mess, from a distance" variety. Also, the Judges are generally pretty hardcore as far as ruthless bastards go. And they regularly see serious action, so they're mostly all essentially veteran soldiers. My comic reading of Dredd is limited, so they may have more up their sleeve too.
Skynet - Remember, this is the system that took over the world. This AI is a the master of gaining control of well protected systems. I could see Skynet running rampant in the Star Wars universe. Also, despite what the movies show, when a well programmed computer is aiming, barring completely unforeseen circumstances, it doesn't miss.
So yeah, there are a fair few good contenders.
Predators would be my top, because in any universe they could hide you well and when not restricted by honour they are very hard to stop/deal with. Especially if they get home field advantage, then other teams that don't have their own ships have pretty much zero chance of finding you, so really only Star Wars would have a shot.
In contention with a lot of people, Vader would be one of my bottom choices. On his home field everyone gets the ability to come after you, everyone here is a good hunter and Imperial security is not exactly top notch vs infiltration. He has easily exploitable and obvious weaknesses and not much in the way of counters to others. Even if you let him use the force on everyone, force sense is notorious imprecise (it is VERY vague), still not much he can do against kamikaze Predator, still vulnerable to EMP, metal Colossus doesn't need to breathe (so force choke is moot), he can't defend much against telepaths, can't stop overwhelming fire, can't do shit to stop Liz Sherman burning him to death. He does have his Storm Troopers yes, but he is an arrogant motherfucker who likes to go after his prey personally without much of a guard force.
PS - Starfleet Command should have been in there instead of fuckin' Marv.