re: Favorite Tom Cruise movie(s)

Taps (essentially the first significant film for both Cruise and Penn - in a support role, Cruise almost steals it.)

Top Gun

Collateral (his best performance to date)

Tropic Thunder (a cameo on steroids, but I really enjoy the film and his role in it)

Color of Money (unlikeable guys like him, Pine, Bale, would do well to stay with antagonist or at least intentionally unlikeable protagonists)

Rain Man (he could have looked bad opposite Hoffman, but he held his own)

ETA: A Few Good Men - probably the best overall Cruise movie - should have been in my initial list. Everybody nailed it and that helped tremendously - Jack did steal the show, though.

Jerry McGuire (the closest I've come to liking a character played by Tom Cruise)