Speaking from personal experience only,
Aged well: M.A.X. (the first that is, the second is made of suck), Homeworld series, Space Empires series, Total Annihilation, The Settlers series (except Heritage of Awfulness), Mechwarrior 4, MechCommander 2, Europa Universalis II engine games, Ground Control (the first), Command & Conquer/Red Alert/Dune serieseseseseses, Operation Flashpoint, Sid Meier's Alpha Centauri
Aged poorly: Dune 2000 3D, Medal of Honor (the original), Grand Theft Auto I+II (and III a bit), Age of Empires I+II, Heroes of Might and Magic I-III (IMHO), No One Lives Forever, Civilization I+II (and III, to a certain extent)