I'm going to say the Green Goblin (2002) because the character was fleshed out and well-acted, also he was a pretty good/insane villain. Looking back at the costume it was kind of cartoony but it did not take away from the overall character.
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My top ten are:
3. The Flash
4. Moon Knight
6. Captain America
10. The Traveler
I have three characters; Spiderman, Superman and Cap that appear in my list and yours.
I disliked both incarnations of these villains for there representations as well as the fact that they were both just through into the plot/story for no real reason; Venom because he is a fan favorite, he would attract more moviegoers and Green Goblin to kill Gwen and introduce the sinister six. Although I am not a fan of these two in their movie forms, the better villain in my opinion is Harry Osbourne/Green Goblin simply because the character was better acted and his character was more fleshed out than Venom. So I will go with Green Goblin.
The train sequence in SM2 was definitely action-packed and pretty great but the Clock tower sequence was more impactful with the death of Gwen and the action by Garfield at the end with Gwen's death was just perfect. It's a close one, but for me the edge is given to TASM2's clock tower sequence. Now if the Electro fight is also included then TASM2 for sure wins, the visuals and fight sequence was fantastic!
I kinda have to agree that it was on sided towards dc. Even though I prefer marvel to dc. But I found it especially in the tv section it seemed one sided.
I voted DC for tv simply because when it came to animated series and tv shows DC wins and I was surprised when I didnt see Justice league unlimited but it's actually mentioned when you look at Batman Animated series but it deserved its own section.
I also thought that for villains they could have given it more diversity instead of just superman and batman villains for dc.