MoO 2: Love it. One of my favorite games.
Disciples 2: Love it.
FF 3/6: Never played any FF.
Civ 2: Love it, although I prefer 4 and 5.
Doom 3: played only a little, looking forward to trying it with the Oculus Rift.
Thief 1 & 2 (3 was a serious letdown): Never tried it, I'll stay away from 3. (3rd syndrome?)
Dishonored (both routes, it seems a seminal work to me): Haven't tried it yet.
Terraria: Haven't tried it.
Minecraft (yes both, they're very different in more than just visual fidelity): Have it, played very little.
Legend of Grimrock: Have it, have yet to try it.
Rez: Haven't tried it.
Penumbra (or Amnesia, but Penumbra worked better for me): Have amensia, and haven't yet tried penumbra.
Hero's Quest (Quest for Glory) 1&2 (the original CLI; none of this fancy mouse interface business!): Some great memories. I remember having to type in all my commands.