I think the one I miss the most is probably Dark Reign, an RTS very heavily inspired by (i.e., ripped off from) the Command and Conquer series. It didn’t bring very much new, but what was already there, it refined to perfection. I’d definitely still play that one if I could.
Another great one nobody has mentioned yet was Myth II: Soulblighter. It was real-time-tactics (like RTS, but with no base or ability to train more units), with great physics, engaging missions, and a strong storyline. My favorite aspect of it was that if you kept your soldiers alive, they gained experience and improved (in subtle and realistic ways), and they kept that experience into the subsequent missions. I also didn’t realize at the time, since my computer wasn’t capable of it, but on max settings the graphics were absolutely amazing.
Of those others have mentioned, I’ll second Baldur’s Gate (still the best computer D&D game) and Chip’s Challenge.
In retrospect, there’s one feature that three of my four favorites had in common: They were real-time, but let you pause the game and give orders to your people while paused, which they’d then follow as soon as you unpaused. I think that system gives the best of both worlds of real-time and turn-based.
most of the stuff I played back then I play now thanks to gog.com and steam …theres still a few they don’t have …(wish sid and take 2 would let them have civ2 gold with updated mp ) …
A few of these games have modern remakes. You can use Dosbox for others, but some are very difficult to get working on any modern computer.
Strategy
Master of Orion I and II - Strategy games in general age well, and these were some of the best in a scifi setting.
Master of Magic - Still the best fantasy 4x game. In a single player strategy game balance is less important than having a variety of interesting strategies. There are dozens of different ways to break it, but that’s part of the appeal.
Fantasy General - Panzer General is more well known, but Fantasy General was very underappreciated for it’s time. Great soundtrack too.
X-COM - I can appreciate both the original and the new ones. Each have their strong points.
Adventure games
Star Control 2 - One of my favourite games of all time. A great mixture of space exploration and adventure. Has a modern port called Ur-Quan Masters with added voice-over.
The Secret of Monkey Island and Curse of Monkey Island - Some of the best from the old Lucasarts collection. I’d play the special edition remake though.
Outcast - An old open world style game. At the time it was revolutionary, but might not hold up that well anymore. There’s an HD remake being worked on.
Others
TIE Fighter - Get the collector’s version if you’re going to play it. It added a large amount of missions, voice-over and other improvements. I’ve heard it can be difficult to get the game working on modern computers.
Thief the Dark Project - Some of the missions overuse monsters, but the stealth missions are pure gold.
One Must Fall: 2097 - One of the few fighting games I’ve ever liked. It’s slower than a lot of fighting games, making it a bit more tactical and less twitchy. Has a campaign where you fight through tournaments and upgrade your robot with prize money.
I wonder if Myst or any of its sequels possess replay-ability, after having not played them for almost 20 years? I mean, it’s not like I recall any solutions offhand.
I played the original Elite too but I had to use hexedit to cheat myself a docking computer, I never could figure out how to dock without exploding on the station wall.
In case that fails, the same developers released a new game called Obduction just the other day, and it’s getting pretty good reviews. http://store.steampowered.com/app/306760/
Master of Magic
Master of Orion
Take your pick of many Sierra Adventures but I will go with Space Quest (and several of its sequels) and Manhunter
The Bard’s Tale
Most of the AD&D Gold Box Games (also the Buck Rogers games which were the same engine)
Sim City 2000
Tank Wars (I got a D in genetics because of this game in college).
Dungeon Keeper
Imperialism (liked it better than Civ honestly)
Alpha Centauri
Arcanum
Baldur’s Gate I and II
Ohhh, yes. That’s one game I wouldn’t mind seeing a remake of. Firing broadsides from a bus was surprisingly satisfying with static graphics an a little text, it could be amazing now.
I think I slightly preferred V to IV, all things considered, but that’s quibbling a bit. Part VII and VII Part 2 were absolutely awesome, though.
I don’t know if it’s my favourite but its from pre-2000 and I still occasionally play it.
Warlords Classic, official remake on iOS of the 1991 Mac strategy game, available for $5 with new maps as well.
I preferred MOO2, but would gladly play either if it was possible. And I’m still going strong with Civ 4 with the BUG mods. I own Civ 5, but it doesn’t do it for me.