I'm replaying Final Fantasy 7, slowly, just a few hours a week tops-still fantastic.
Master of Orion 2 as mentioned, still ace. Star Trek: Birth of the Federations, not quite ace but I still reinstall from time to time- it's MOO2 with Star Trek on top, and less good combat. The race modelling's crude but good- Klingons are always gutted if you make peace with an enemy, even if you're beign hammered, some of the minor races immediately capitulate if you declare war on them, the Federation get upset if you carpet bomb a planet... Basic, but quite effective. Plus, Klingons. And the Borg, who no matter when they turn up will entirely kick your ass.
Transport Tycoon Deluxe... Need to get that new version, I've heard about it but never got round to installing. The original (and the Deluxe) were brilliant despite the bugs and the overall pointlessness.
I might reinstall Mechwarrior 2: Merceneries soon, it was great... And Mechcommander, for that matter, dated now but still cool. I remember when I got MW2:Mercs, I had a P75 with 8mb of ram and we had to upgrade to run it. Feel the awesome power!
The original Homeworld's quite old now as well, and still stunningly good.