UFO: Enemy Unknown (much better game title than X-Com UFO Defense) was a classic. I watched my dad play it on the Amiga for hours on end, I was always too impatient and rather creeped by Chrysilids to play it.
When I finally got my PC, I tried X-Com Terror From The Deep and really enjoyed it even though I still had no grasp of tactics.
UFO Aftershock or Afterlight (cant remember which) was one game I played and it just feels so far away from the UFO: Enemy Unknown we all grew up with and knew. Like RTSes, I dont think something like C&C3 has a patch on the Grand daddy of all RTSes, Dune II: Battle For Arrakis.