Thief controls are still great, they feel "crisp". I think System Shock is fine too, I even like using a mouse pointer to aim and interact with the world. Ultima Underworld I find a bit harder to play.
In Underworld, I use wasdzxc keys for gross movement, and the mouse for finer control. 1, 2, and 3 can control looking up and down. Using the control scheme, rather than relying exclusively on the mouse, makes the game more playable for me.