This is gonna be one looooong comment, ready? Here goes!
I'm gonna cover all the games in this except the one's I haven't played, which is a no brainer methinks.
Super Mario Bros 2: Damn straight! I loved that game! Prefered New Super Mario Bros though.
Ocarina of Time: Quite possibly one of the greatest games out there, especially when it came out on the gamecube as a special edition, which is sooooo hard to get hold of these days.
Tetris: Weird russian band at the end! Nuff said! Also the music was awesome.
Portal: Yeah, evil computers, acid, portals, an fantabulous ending, this game had it all. And some sweet music at the start to!
Lemmings: I sucked at it royally but it deserves a place because of origionality....and the ability to send them plunging to their deaths when your bored.
Bioshock: Hmm... a gripping story, the audio diaries were a nice touch, so were the creepy moments like those multiply staues, or the one that appears right behind you after using the weapon upgrade station...or the evil dentist guy...brr
Katamari Dynasty: Rolling rolling rolling, gotta keep on rolling...hmm? You were saying something?
Donkey Kong: Naaaaah, the big ass ape never did it for me, except in Mario vs Donkey Kong, hey, that should be up there I think.
Super Mario Bros 3: Wait was that the one that had the Racoon suit? Other than that it didn't improve on 2 that much.
Super Mario World: Ahhh....the origional, I loved that, sucked at it but loved it, especially the plane and submarine levels.
Super Mario 64: Your Nintendo fan, right? There's no way so many mario games could be on an unbiased list, still, this one deserves to be there, 3d was a good step for mario, even though Sunshine wasn't as good.
Smash Bros Melee: Just wait until the sequal, it is gonna be epic!
Zelda Windwaker: Booyah! Cel-shaded goodness! And a good game to boot! The final boss battle defied some belief, GIANT PIG!
Super Mario Galaxy: The ice flower, the music that acompanies it was enough to win me over, and I managed to get all the stars! Finally!
Doom: Nope, can't see it being here, now Quake! There was a good game! Especially 4, I can't really remember why though, of course! The high-rez guts and blood!
Guitar hero 2: What is it that everyone see's in this game? Why not just learn to play a REAL guitar? It makes you look like 90% less of a prat!
Zelda: Link to the past: It was waaaaay to long for my short attention span...Oracle of Ages and Seasons should be up there instead, they were better in my opinion.
Zelda Majoras Mask: 3 days...3 days...3 days...creepy? You have no idea. Side quests were fun though, even if no-one remembered you after you had to rewind time. Inside the moon was cool too.
Worms: The origional or one of the sequels? I liked it back when it was one of the older ones, beacause the scenery was a bit more whacked out back then.
Myst: I really didn't understand that game, peaceful though and there was a sense of satisfaction when you figured out what you were supposed to do.
Super Mario RPG: I prefered Paper mario to this one, although RPG did have the better music. I wonder if it will come to virtual console?
Harvest Moon: Its been a while since I played that, loved every time chewing minute of it.
Prince of Persia: The sequels were bad but the origional was a shining beacon of 'Platformers don't completely suck!'-ness. Alright combat as well.
Pokemon: Arrgh! I hate these games so much! What is with these games being so popular! Ever since the first one they've been re-using the same old idea over and over with slightly touched up graphics and some more crappy pokemon to collect.
Kingdom Hearts: No matter what anyone else says, the better graphics, the more replay value, extra worlds, better companions, the origional had the more epic boss battle, I mean sure, in the 2nd there was a huge dragon thingie, but in the first it was a bleedin' planet sized bugger who really, really wants you dead. The who, 'My god! Riku is evil? Oh noes thing is good to, and the fact you get to turn into a heartless at one point, I bet most of you don't even remember that bit!
The Sims: Must burn them all! BWOHAHAHAHAHAH!
Halo3: Microsoft= Money Grubbing, that and the fact they plan on making another, and another, and another... seriously, watch through the credits and you find out that Master Chief ain't dead! OMG! NO WAYZ! Now we have to play through another crappy sequel with little or no plot and without the psycho computer which sounded brilliant.
Things I think should have been in there:
Starfox Adventure: The best graphics on the Gamecube ever!
Neverwinter Nights 1 or 2: I loved every minute of these games from the start of winning the harvest cup (2) to fighting evil lizard queen at the end of No. 1 there was nothing but virtual dice throwing goodness.
Age of empires: The 3rd one most probably, the introduction of guns is a huge tactical advantage. And they are far better than arrows.
Morrowind: And yes I know Oblivion has better graphics, but its so, small! And I hanker for some cheap goblin smashing goodness for the cheapest price around! The whole 'Turn into a werewolf' thing was cool to.
Tabula Rasa: An MMO that tried to revolutionize the way you play and sure it failed epically, but the most important thing is that it tried, and came out with a pretty good game too.
Mario Kart: BLUE SHELL OBLIVION! Sure its cheap, but watching the agony on your friends face as they drop to dead last is priceless, at least until it happens to you.
Meteos: It's like Tetris except upside-down! Ooooooh, I love the sense of panic when it doesn't quite make it.
Mario Football (Wii): Kick the crap out of people, ONLINE! It also offers a good, steady learning curve in the main campaign and some kick arse captains.
Soooo....I think i'm done here, this better total up to an impressive list.
Anyways, the Hammerypart says: Cya 'round!
ConAir
Great list so far, I ctrl+F'd a few games and found out you had all of my favorites up there too (myst, KH, portal, etc.) ...except one - GTA 3, probably one the biggest landmarks in gaming of all time and definitely one of the best. I think it deserves a spot somewhere amongst all the greatness, unless there's a reason you didn't put it up?
While I'm at it, was Halo 3 seriously one of the best of all time? For what, the replays? I'd say one Halo's enough to cover the whole series, but series that are so different like Zelda OoT and MM definitely deserve separate spots.
jmtb02
Halo 3 for multiplayer... it seriously changed the standard of how multiplayer gaming works. For that matter, Halo 2 might have been a better choice, but Halo 3 mastered it.