I decided the only way to really find out is a tournament. Thirty-two villains step into the ring, two-by-two and fight it out. I created a bracket and randomized the entries. A few of the villains I've covered in my series won't be admitted here - Emperor Dark for not doing anything for his whole series, Dr. Claw for being mostly hidden through his series, and Baron Greenback for being a tiny toad. Unicron and Cobra-La are also out since they both kind top the charts. But the rest of the contenders can be seen here:
For each fight, I'm going with Death Battle rules - I'll be watching each show and take notes of each villain's powers and abilities. I'm limiting myself first 13 episodes of each show to be fair to those shows that didn't make it that far. Each round will be made in two posts - the first week will cover the villains' abilities through the episodes, and the following week will have the results, told in a short story since I'm not about to try to animate this. I wish I had some way to show it better, but I'm hoping to at least draw some picture of the winner triumphant.
Of course, I welcome everyone's comments on who they think should win, and I'm looking forward to hearing any disagreements, but please realize, this isn't going to be a popularity contest. If it was, I'd automatically make Megatron the winner. But I'm curious who really kicks the most ass here and I want to be as impartial as possible.