Nintendo Entertainment System (NES)
1. Super Mario Bros. 3
2. Mega Man 3
3. The Legend of Zelda
1 is fairly safe. LoZ, MM3, and MM2 are all pretty much tied for #2 depending on mood, but I'll tiebreak for MM3 because more stages + a non-stupid passwording system, unlike MM2 which robbed your energy tanks. Dragon Warrior 4 is probably the best RPG on the console, which deserves some credit... as does Zelda2: The Adventure of Link and Super Mario 2.
DOS/Windows 3.x PC
1. Civilization
2. Frontier: Elite 2
3. Railroad Tycoon
Uh, for me, this will be the "Amiga" section. Still, pretty much most of the Amiga games were also on DOS, just with worse graphics. Note that I played SimCity and Populous on the SNES, not on the Amiga, so not including them here. Railroad Tycoon is kinda shaky, as SimCity would certainly beat it - but having trouble coming up with good competitors at the moment. Secret of Monkey Island would probably qualify, but I'm playing the Special Edition of that *right now* on Steam since I didn't catch it on the Amiga, and I never would have gotten anywhere anyway when I was young and foolish. In terms of time spent, I think that Red Storm Rising would come the closest to knocking off Railroad Tycoon, actually. Submarine combat is fun.
Also, looking at OK's list... Civ 2 and MOO2 would certainly invade #2 and #3 if I felt they belonged here. But eh, I associate them with the Windows 95 era, although I know that MOO2 at least could run in DOS 7. Edit: Colonization! would also easily make #3 too, since I saw somebody else list that in this section. But I played the Win95 version of it, not the Amiga one, so.
Super Nintendo Entertainment System (SNES)
1. Final Fantasy 3 (6)
2. Chrono Trigger
3. The Legend of Zelda: A Link to the Past
I could very, very easily have stuck Final Fantasy 2 at number 3 instead of LoZ, showing my RPG fanboy side. Super Mario World and Secret of Mana are up there as well of course.
Sega Genesis (Gen)
Go Sonic 2 and PS3?!
Windows 95/98/2000 PC
1. Heroes of Might & Magic II
2. Sid Meier's Alpha Centauri
3. Myth: The Fallen Lords
Pretty easy. Heroes of Might & Magic III is easily number 4. Myth II is weird as it is by all rights as good as Myth I, but feels a bit like an expansion pack since it came out just a year later. Civilization II is probably 6, but SMAC is just better as Civ2 required mods and such to keep it interest. Blizzard RTS (StarCraft, WarCraft III) are decent but mostly on multiplayer hype grounds, but I feel both Myths did a much better job at both single-player and multiplayer. The Longest Journey and Curse of Monkey Island are also both tempting here as far as adventure game hype, and Deus Ex and Unreal Tournament get shooter hype. Also uh Final Fantasy 7 and Final Fantasy 8 technically fall in here too, for me.
Sony Playstation (PS1)
1. Final Fantasy Tactics
(DROP)
2. Final Fantasy 7*
3. Front Mission 3?
#1 is easy. But wow this drops off after that. Much as I like them, none of Lunar, Castlevania: SOTN, nor Front Mission 3 feel like worthy top 3 slots. Nor for that matter Threads of Fate, Grandia, Xenogears, or Metal Gear Solid. So screw it, sticking FF7 here anyway despite playing the PC version, add Lunar or Castlevania to replace it if you want. Final Fantasy 8 would be in the ToF-XG-MGS tier, mind.
Nintendo 64 (N64)
1. The Legend of Zelda: Ocarina of Time
2. GoldenEye
3. Super Smash Bros.
I technically played Ocarina of Time on a GameCube, but yeah, it was basically a straight port of the N64 version (didn't bother with the Master Quest), unlike say SimCity where the SNES version has better graphics and more features than the PC version. Also, I didn't own an N64, but I did play through all of GoldenEye & Smash's single-player.
Gameboy Advance (GBA)
1. Fire Emblem: The Sacred Stones
2. Fire Emblem
3. Castlevania: Aria of Sorrow
I've played exactly one GBA game legit, and it's the one I'm going through right now: Metroid Fusion. Can't really recall what other GBA games I've played other than the above, so I might switch 3 around. Castlevania: Circle of the Moon was pretty decent, though, and is not that much worse than Aria of Sorrow. (Edit: I guess I played Metroid: Zero Mission too as a loaner.)
EDIT:
Dreamcast
1. Grandia II
2. Skies of Arcadia
3. Shenmue
This is pretty easy, having played just 3 DC games. Well, maybe 30 minutes of Jet Grind Radio too I guess, but no.
Playstation 2 (PS2)
1. Suikoden III
2. Shadow Hearts: Covenant
3. Final Fantasy X
1 and 2 are basically tied. FFX has very strong competition from both Growlanser games (II & III), Tales of the Abyss, and Xenosaga: Episode III... FFX and XS3 are a lot alike, actually (said to make Elves rage), and "the best parts of Xenosaga combined" would take #3, but XS3 has some issues in its later half which FFX handles better. (And I don't mean issues I find stupid but ultimately irrelevant like KOS-MOS plot, but bigger lapses like Wilhelm plot.) That said XS3 feels more replayable than FFX, since characters are a bit more customizable, but I never replayed either, so hmph. Also MGS3 hype here but no room.
XBox (XBox)
Uh I played through Halo, and played KOTOR on the PC, and played most of Panzer Dragoon Orta at a friend's house, but no vote.
Gamecube (GCN)
1. Fire Emblem: Path of Radiance
2. The Legend of Zelda: Twilight Princess
3. Eternal Darkness: Sanity's Requiem
Another tie between 1 and 2. Super Smash Brothers: Brawl and Tales of Symphonia are both strong runners-up for slot 3, they're pretty much tied with Eternal Darkness. ToS ultimately it kind of outstays its welcome, and Smash only loses because I'm not ultimately a huge fan of fighting games, for all that SSBM does it exactly right as far as my fighting game tastes are (no memorizing button combos!). Also, see above note on Ocarina.
Nintendo DS (DS)
1. Phoenix Wright: Trials & Tribulations
2. Radiant Historia
3. Castlevania: Order of Ecclesia
Slightly me intentionally mixing genres, as picking is hard here. Hotel Dusk and Ace Attorney Investigations: Edgeworth could both easily take 2 & 3 if I wanted to fill all the slots with adventure games, but Dusk's gameplay is too lacking and if I had to pick one PW game, I'll go with the one with the best villains.
Playstation Portable (PSP)
1. Wild Arms XF
2. Final Fantasy 7: Crisis Core
3. Dracula X Chronicles: Rondo of Blood
Kind of a 3-way tie, almost. Only 3 PSP games I finished, makes it easy.
Windows XP+ PC
1. StarCraft II
2. Team Fortress 2
3. Dreamfall: The Longest Journey 2
Time to go with Steam games and really recent games, I guess. SC2 and TF2 are both a blast multiplayer. Dreamfall has a great plot and at least inoffensive gameplay, unlike Hotel Dusk's "annoying" non-gameplay. Does Portal count here? Probably. It's great but short, so I'd still stick it as #4. Civ 4 might sneak in as number 5, but hard to be objective there - I frankly played too much Civ / SMAC when young so never played too much Civ4.
360:
No vote, but I did finish Halo 3, so it'd win by default.
Playstation 3 (PS3)
1. Heavy Rain
2. Final Fantasy XIII
3.
(Valkyria Chronicles? Mega Man 10? I've finished neither of them, although with MM10 I got to Wily's castle at least... haven't started MGS4 yet.)
And I've only finished 2 PS3 games.