Joker- Batman Beyond: ROTJ (the flashback death)
*Darkseid- Justice League "Twilight"
Admiral Zhao- Avatar: The Last Airbender
Starscream- Transformers: The Movie
*The Shredder- TMNT 2K3 "Return to New York" Part 3
*Slade- Teen Titans "Aftershock" Part 2
*Solomon Grundy- "The Terror Beyond" and "Wake The Dead"
President Luthor- Justice League "A Better World"
*Felix Faust- Justice League "Paradise Lost"
*said villains ultimately came back.
really can't think of many villain deaths that held.
Scar from The Lion King was great just because he was such a jerk and I was glad for him to die.
Zabuza from Naruto was another jerk who got what he deserved, even though he redeemed himself at the end.
Cell from Dragon Ball Z was great as well. Finally the crew was able to beat someone without Goku. Even my favorite guy Vegeta got in on a piece of that action.
Vegeta's death in the Kid Buu Saga was another great one. I actually refuse to watch any further episodes of Dragon Ball Z. As far as I'm concerned. That ended the series.