7. Cyclops - X-Men: The Animated Series
Ok, so, from the off, obviously Cyclops isn't a comic book villain. Has he been a stick in the mud? Yes. A bit of an antihero? Also yes. But for Wolverine specifically it's more than fair to say that Cyclops has been a villain.
The two are good friends - great, wonderful friends, even, judging by their sleeping arrangements on Krakoa! - but back in the day all Cyke was to Wolvie was an obstacle standing between him and Jean, as well as a leader who played things too much by the book.
X-Men: The Animated Series did a remarkable job of sticking close to the comics, and one of the elements it best conveyed was of course Logan and Scott's combative relationship. These two really did not get along, and it was made clear right from the off, with Wolverine comically punching Cyclops after the X-Men's mission to take down the Sentinel program resulted in the capture of Beast and the death of Morph.
In context the punch packs an emotional wallop, but without it, it's just absolutely hilarious. God knows how Summers was able to recover after this one.