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Apropos System Shock, the sequel runs fine in wine, and is easier to enjoy, because they use the modern fps controlling conventions. Thief: The Dark Project uses a the same engine as System Shock 2 and is also worth playing.

If you are going to play X-Com: Ufo Defense, you owe it to yourself to use XComUtil [1]. XComUtil patches the binary to remove some bugs and can optionally introduce new gameplay elements.

Also the original Master of Orion is still one of the best civilization type games, if not the best. It has aged well, and really shines in its concentration on large scale decisions, and avoidance of micro-management.

[1] http://www.ufopaedia.org/index.php?title=XcomUtil

If you're on a Mac and like extra-fancy UIs, there's also the DOSBox-based Boxer: http://www.boxerapp.com

There is an RA1 reimplementation called OpenRedAlert.