While he's never made a truly great film, he's taken a lot more chances with his acting than people give him credit for. Born on the Fourth of July and Interview with a Vampire were much gutsier choices (whatever you think of the results) than anything, say, Harrison Ford has ever done.
I'd say the film that best showcased the qualities that made Cruise a star without making you sit through "a Tom Cruise movie" (i.e. Cocktail) was The Color of Money. Among its other pleasures (i.e. Newman's acting, Scorsese's direction, Mary Elizabeth Mastrantonio's panties) was an unforgettable one-scene performance from Forrest Whittaker.