how could I have missed this thread?!
anyway, it's hard to choose the very favourite as different games have different flavors. I'd choose "champions" and "elites" as a runner up category.
Science Fiction:
Champion: Mass Effect. in my eyes the game is unlike anything before it and showed that a s-f setting can handle an RPG just as well as fantasy. involving story, awesome characters (WREX! SAREN!

), interaction, moral choices (paragon vs renegade as opposed to good vs evil most games use; you're still doing the right thing, it's all about the "how" in this game). Another point that makes me choose this over the KotOR games is that it creates it's own setting instead of using one that's been developed by throngs of people for several decades.
Elites:
Deus Ex - it's an awesome game, however revolutionary in it's own way, it kind of pales in comparison to ME
KotOR - both, tho I prefer part 2 by far, Kreia owns
EVE Online - something about it just doesn't fit for me, probably the intimidating scale, it's just too much for me
Final Fantasy 7 - it's one of the few console games that really got on my good side. while it's painfully linear, the story is pretty awesome, and contrary to the chibi character representation, it's quite dark and pessimistic. the game sports some of the most memorable characters ever made (AERITH <3). also, Uematsu's music is pretty damn awesome as well. the downsides would be the ridiculousness of some monsters (come on, a walking doll house? man!)
Fantasy:
Champion: this is probably going to be controverse, however... World of Warcraft. It has it's own faults, fair enough, but it's one game that has done for it's genre the work jump that no other single RPG ever did... from a niche to a mainstream powerhouse. the game offers a SHITLOAD of content, some of it quite dated, but nevertheless a combination of quality and quantity that, along with the ongoing expansion and content patches, keeps the game going for way over 4 years now and it's still going to go on for a few more years at least. the game is hardly revolutionary in most of it's technical aspects, however bringing it all together into one game in this manner was like hitting the jackpot. it's the game that stole the most time of my life. it also has an incredible music score; a great most of the tunes in the game are really top-notch work out of any game out there. however, with other games that I'd like to mention, it really wasn't an easy choice.
Elites:
Baldur's Gate series - BG1 was the game that brought the cRPG back on it's legs after years of stagnation. it's sequel has the rare virtue of actually being a lot better than it's predecessor. both are awesome games that kept me playing for months.
Planescape: Torment - possibly the best cRPG at it's core, Torment was a real blessing from whatever gods that might exist for me. a dark setting, a dark story, an unusual protagonist, all the elements of the game create a whole that, to me, was like reading an intellectually challenging book or watching a tough film, only a lot better - since you're in the middle of it all and not just a bystander. it receives bonus points for making stats like Wisdom, Charisma and Intelligence important for _ALL_ characters. creating a hulking ugly retard was just suicide, where in BG it was the easiest way to get through the game. the music is simply incredible, and when I recall some of the tunes in my head, memories from the game flood my mind and I fade away from the world for a bit and remember the story, the characters... all in all, this game is exceptional
Morrowind and Oblivion - both of these got their strong and weak points in comparison to each other, so I just have to throw them in as a single game, really. an open-endedness with few to rival, both games have vast amounts of replayability. there isn't that much to say about them come to think of it, it's hard to explain to someone who didn't play them at all, and those who did know exactly what this is about
The Witcher - I may be biased, being a long-time (been 10 years now) die hard fan of the books from the setting it's based in, but the game is simply awesome. it captures the essence of the setting perfectly, the morals, relations between races, viewpoints, dilemmas... everything. it does perfectly what that shitty pile of a movie failed to. the fighting system and camera angles, as well as fighting animations, make for a great feeling during action sequences throughout the whole game; it never gets boring.
Diablo series - I just have to mention these. I'll probably come through as a Blizzard fanboi, but the 2 Diablo games are milestones in the action RPG branch of gaming, as well as playing action RPGs online wtih use of the battle.net server. both Diablo games offer an easy-to-get-into experience, with a balance between the two parts - the first one's atmosphere was a lot darker and more to my liking, while the second one has superior interface, game mechanics and a lot more content. again, like with all Blizzard games, the music is simply awesome and the very highest quality range of any game music ever made. just recall the Tristram tune

Neverwinter Nights - an awesome transition of D&D from a party to a single / two- character game. NWN is plenty fun and it's annoyingly consuming. it doesn't seem like much but it can turn the afternoon into the middle of the night without you noticing the passage of time. also, it has a great modding community, many of the mods are actually better than the original campaign. it has it's faults, but it's still one of my favourites.
This post has been edited by Gothos: 17 June 2009 - 11:19 PM
It is not the critic who counts; not the man who points out how the strong man stumbles, or where the doer of deeds could have done them better. The credit belongs to the man who is actually in the arena, whose face is marred by dust and sweat and blood, who strives valiantly; who errs and comes short again and again; because there is not effort without error and shortcomings; but who does actually strive to do the deed; who knows the great enthusiasm, the great devotion, who spends himself in a worthy cause, who at the best knows in the end the triumph of high achievement and who at the worst, if he fails, at least he fails while daring greatly. So that his place shall never be with those cold and timid souls who know neither victory nor defeat.