Con Air was a funny decent watch if you don't think about all of the plot holes. Only John Malkovitch movies that I like him in were Red, Red 2, and Dangerous Liaisons (but what was there not to like about that last one). He was a despicable character in in the Line of Fire, which like in Con Air he does well.
I remember seeing Valley Girl, but really don't remember it very well except he had weird chest hair.
A guilty pleasure for me was The Rock, but that had Neil Harris and Sean Connery in it as well . I also really liked him in another guilty pleasure movie - Moonstruck. Again had Cher, Danny Aiello and Olympia Dukakis.