Let's see what I got.... Note that spoilers are included but I am not going to put a spoiler tag everywhere.
1. Kuja Tribal (Final Fantasy 9) - It was a really tough choice for me to choose between both Kefka and Kuja, but I like the second just a bit more. A very powerful character who had the abilities to whipe out all of existence. He even managed to do so, but his plans were spoiled by a final boss who shouldn't be there. Darn you Necron!!! Oh, and Kuja has also never been defeated by the protagonists. Never. And his role in Dissidia was pretty interesting too. If Kuja wouldn't have been there, Kefka Palazzo would probably take the top spot. But Kuja deserves this place.
2. Dr Ivo Eggman Robotnik (Sonic franchise) - If it weren't a list of video game villains, Eggman could have competed with Kuja. But still, his accomplishments in the games weren't too shabby either. He unleased several demigods of destruction on the world, as well as the creation of several robots, including Gamma, Omega and Metal Sonic. And he is just plain evil, as he did blow up the world. And also accidently almost destroyed them if it weren't for Sonic.
3. Ghirahim (Zelda: Skyward Sword) - I could go for Ganondorf but nah, Ghirahim is complete nuts. And I like insane characters, so this spot was reserved for him. He's a strong villain too, parring with Link at times. Of course, Link has the protagonist curse so he will always win. But man oh man, the battles with him were good.
4. Fawful (Mario & Luigi series) - Bowser? Nah, he's a joke of a villain. Fawful is just plain nuts, awesome and powerful. Also points up for surviving exploding in Superstar Saga and then return as the main villain in Bowser's inside story. Good job, boy.
5. Glados (Portal Series) - Mean, cruel, hilarious, insane. Everything a villain should be.
6. Dr. Wily (Mega Man franchise) - Aah, good ol' Wily. Probably some of you see him as a... pretty bad villain because all he has done was reprogamming robots and failed everytime. Eh, reprogamming is already a nice feat, but what put Wily up here are the following reasons: He created Bass, the Yellow Devil and Zero. And with the creation of Zero, he also made the Maverick Virus (correct me if I'm wrong here) which was passed on to Sigma. Wily, while dead, played a huge part in the events of the Mega Man X, Zero and ZX series. That's just awesome.
7. Cyrus (Pokemon D/P/P) - Wants to use the creation trio (Dialgia, Palkia, Giratina) to rewrite the universe to his bidding. Now that's pretty genius. Of course, he loses to a 10-years old pokemon trainer and after the battle he just gives up all his plans. Pokemon logic, don't question it.
8. Duke Polentei (Tales of Vesperia) - I haven't played all of the Tales of games yet, including the most popular ones. So please, don't hurt me. I just like Duke a lot because he is an omnious and very powerful character. And he is not particularly evil. He just hates mankind. I don't blame him.
9. Vaas Montenegro (Farcry 3) - Ehh, I'm not the biggest fan of current generation villains. Especially not in shooters. But Vaas is just a genius. And insane, that's why he's on here in the first place.
10. Senator Steven Armstrong (Metal Gear Rising) - Probably one of the most hilarious political statements ever made. I think The Autarch of Flame describes it best in his video