Baldur's Gate 1+2 (especially with the mod that combines them!), Planescape Torment, Evil Genius, and the Gothic series of games. I think in general RPGs hold up pretty well compared to other genres.

Freespace 2, hands down. Especially with FSOpen: Redeemed

Many of the already named games and
Crusader: No Remorse/Regret

BG2 the backgrounds are still gorgeous
MOO2 solid gameplay and while the graphics are pixely, they are still nice
Uplink The game is a computer screen lol
Imperialism solid gameplay and decent graphics
KoDP wonderful gameplay with beautiful artwork
Shogo MAD very playable

If you have the ability to ignore the graphics and learn the controls/UI I think 99% of old games are playable.

With that said I would have to say these games have not aged well: (I choice not instead of listing the games I do like consider the numbers I'm okay with)

Ultima 6 and earlier
Fallout 1
Outcast
MDK

Ultima games I unfortunately only judge from graphics and mechanics alone so I guess in theory I could enjoy them but I won't make an effort to try them for now (I'll likely will down the road).

The other three has technical issues that is possible to solve by patches and time but so far it wasn't enough for me to bother playing after trying them to work optimally.

Anyone mentioned Settlers 2, yet?
Maybe the remake, 10th Anniversary, too.

I'll third this, because the graphics and sound simply don't matter. The gameplay itself is enough to stand the test of time, regardless of what it's wrapped in.

For the same reason, I add to the list Master of Orion.

Alpha Centauri has aged really well, and I am really loving my first play through of Planescape: Torment although I don't really know how well it's aged per say (I mean general stuff like graphics and resolution options and occasionally crashing to desktop) and the combat still isn't very good. But the story, writing and characters (which were the real strong point of the game anyway) are just as good as they've ever been.

Good old DOS (Windows games are to me "new") games that I've played or replayed recently, and enjoyed:

Might&Magic 1-5
Ultima 5 (but not 4, 6 and 7)
Starflight 1 and 2
Wizardry 6 and 7
Ultima Underworld 1 and 2
Darklands
Betrayal at Krondor
Lands of Lore 1
Master of Orion

Not sure if any of them count as old but... Torin's Passage, Syberia (granted it seems point and click games age pretty well in general) I havn't actually set aside the money to try many others just yet, but hopefully I can come back with a much larger list before too long

I played many of these games when they were originally issued. Master of Magic did indeed retain all its interest.

The same can be said about Subwar and Master of Orion II. Many former Microprose titles are still very good nowadays ( beside the ones found on GOG, the XCom series, Machiavelli and European air war 1943 ... )
We have to agree to disagree on those. While I would indeed leave ultima IV and earlier rest in peace, V and VI are worth, imho, going beyond their obsolete appearance.

IMO (I haven't seen the entire list - so forgive me if a few of these are repeated)\

1)Bg1 + 2
2)Icewind dale 1+2
3)Jedi Knight 2:Jedi outcast(Not on gog but worth a mention)
4)Kingpin - best looking game on the quake 2 engine albeit a heavily modified one (very playable even today)
5))Disciples 2 and homm2 +3
6)Omikron:the nomad soul
7)clive barker's undying - still looks pretty darn good
8)Alpha Centauri
9)Battle realms:winter of the wolf
10)Beyond good and evil
11)blood 1
12)stronghold crusader + stronghold (both in hd now)
13)TOEE
14)Vampire the masquerade redemption (wish bloodlines was here_
15)Freedom Force & freedom force vs the third reich (you should try this if you enjoy comic books or like superheroe lore in the slightest)
16)KKND
17)xiii (unfortunately, it is no longer being sold now -here on gog)
18)Darwinia. Defcon, Multiwina, Uplink ( all very original and interesting games
19) Sanitarium (one of the few adventure games that I like)
20)Startopia
21)Prince of Persoa:Sands of time etc

I honestly don't get all this HD craze, and people *having* to play -- mostly Infinity Engine games -- in "glorious" HD... I've seen Fallout 2 and Planescape: Torment being played with mods and fixes, in high resolution, and, in all honesty, aside from the fact we get to see more of the field, it seems like we're playing with a tiny stick man. That's definitely not how the developers wanted us to see their games... crafting those sprites/models took time and dedication, and now all people want is to almost not being able to see them, just for HD's sake.

These games actually aged pretty well, there's no need of any kind of HD treatment to enjoy them better.

Agreed,groze, I also always play those games in the original resolutions,even on a 27 inch screen.

As for aging well, I think most 2D games don't age much, if they have an ok interface, then I can play them forever. Still play many 20 year old Amiga/Dos games regularly, like MadTV!, 1869,Keef the Theef,Transarctica...think some of them are very beautiful.