No, the Coyote never ate the Road Runner. He did, however, catch the bird in one cartoon, produced in 1980 by creator Chuck Jones. That film, Soup or Sonic, was part of a TV special called Bugs Bunny's Bustin' Out All Over. In that film the Coyote shrinks to tiny size but manages to grab the Road Runner's giant (to him) leg. Unfortunately the Coyote is like a tiny insect to the bird. He holds up a sign to the audience: "Okay wise guys, you always wanted me to catch him. Now what do I do?"
It's almost like a vindication. I sooo remember seeing this. I remember the sign he held up at the end... I've asked tons of people and they all thought I was on crack... No one else knew of this one. I guess that's what I get for watching all the Bugs Bunny specials.
Wow this really is shaping up to be a great year.
( http://www.straightdope.com/columns/read/2297/did-wile-e-coyote-ever-catch-the-road-runner-plus ) if you want to read about it yourself.