He was chasing Road Runner and gets hit by a truck in Bumbie's Mom.
In "One Flew Over the Cuckoo Clock", Wile E. is seen at the hospital in a wheel chair (however, his face is not shown).
Wile E. also appears in in a The Wizard of Oz parody, dressed in his batsuit from one short, in a tornado funnel in "Buttons in Ows".
He is among the cartoon characters seen in Dot's musical number in the reboot episode, "Suffragette City", where he is seen with a smug-looking face and holds up a "Vote!" sign as Dot mentions him.