First games that come to mind:

Populous : The Beginning
Dungeon Keeper 1
and this masterpiece

Games that were good that continue to be good is fairly easy, but timeless is a bit trickier.

I might submit, Final Fantasy Tactics? Farcry? I can't seem to think of a time when Hotline Miami might not be fun anymore. Viva Pinata? Professor Layton and The Curious Village? Rome: Total War? Metal Gear Solid? No One Lives Forever?

I've got it, Mario Tennis.

Nailed it.

Thanks to you the soundtrack is stuck in my head now. :`)

This song

Oh, and Kirby is always fun to play.

To me it's hands down the Disney film with the best Soundtrack :)

My favorite is This Land

Cel shading was a breakthrough for 3d games. Something like Megaman Legends manages to continue looking great while Tomb Raider 1 (which only came out a year and month prior) suffers immensely. I think any game that has pulled off ancient era 3d and is still charming today is timeless. :>

I'd have to go with;
Monkey Island 1-3
Riven
Commander Keen 4-6 and Dreams
Descent 1-3
The Dig

Prince of Persia (the original)
Bubble Bobble

Diablo

No love for Commander Keen 1-3?
2 was ok, and 3 pretty meh, but 1 I think is still a solid and fun platformer.

By the way, that's an awesome avatar! I'll drop you with my my dual Heavy Gauss + dual ER PPC Fafnir tho ;)

diablo was never good to begin with tinyP ;p

yes i am glad you agree
calling diablo good is blasphemy ;p

Golden Axe. Especially the 2 on arcades (Death of the Death Adder).

Super Mario All Stars for Snes.

Super Mario World 1 and 2 (yoshi's island) for Snes.

Sonic 1 for Genesis (plus the rest sonic titles for same console).

Castlevania Symphony of the Night and Legacy of Darkness (the first 3d title of series and first game in which final boss was in full power, this one).

Super Mario and Wario Land games for Game Boy.

Pokemon Gen 1 and 2 for Game Boy.

Diablo 2 plus LOD.

Red Alert 2 plus Yuri's.

King of Dragons, Warriors of Fate and Knights of the Round, for arcades, of course!

Dragonball Z Super Butoden series and style of this series, across many platforms (it was on Genesis, Snes, even PS1).

Blade of Darkness. 15 years passed and feels and plays as good as new! Too bad GOG removed it.

Vampire the Masquerade series. Especially Bloodlines, which according to fans: "It doesn't age, it is immortal"!

Mortal Kombat 1, 2, 3. Seriously, i can't wait for gog to release Trilogy, already!

Thief 1 and 2!

And that is all about my educated list!

Magic Carpet (and the sequel too, I guess).

Warcraft 2
Diablo 1 and 2
(Yeah, go classic Blizzard! :P )
Doom (well pretty much all the games off of this engine too)