My Vote is for... (And YA'LL SHOULD BE ASHAMED FOR NOT MENTIONING IT.)
Freespace 2.
Easily the Pinnicle of Space-Sims on *any* platform, Freelancer refined it, Star Citizen (Potentially) revolutionizes it.
Otherwise... Master of Orion 2 (Let's ignore 3 and pay attention to the latest reboot. :P)
Alpha Centauri. - Civilization: Beyond Earth promised to be a spiritual successor, but ultimately fell short IMHO.
Dungeon Keeper 2. - It's good to be bad. (The mobile game doesn't count, right?)
--::{PC Gaming Master Race}::--