I have to say that the older I grow the more I realize I have never really experienced a game who's villain has resonated with me long term. I guess I used to be pretty into Halo's story, and those campaigns still have an impact on me when I think about them, but there are so many different villains over the course of that series.

So unfortunately I'll say none. I don't really think gaming has resonated with me from a story perspective as much as it has with others.

Wario, he is definitely number one. Number two goes to Man-bat from Arkham Knight.

Hmmm. Definitely The Illusive Man from Mass Effect.
Twilight Princess Ganondorf.
Albert Wesker.

Kefka from Final Fantasy VI is my favorite. He's cruel, ruthless, and accomplished his goals.

Kain from the Legacy of Kain series (Soul Reaver are part of it)

Kane from the Command and Conquer series

Ganondorf (and, by extension, Ganon), the great hijacker from the Legend of Zelda series.

The Duck Hunt Dog (he's just snickering at you for reading this!)

Kreia/Darth Traya from KotOR 2. Major spoiler if you haven't played it yet, so if you want to play it sometime, please avoid looking the spoiler. 

Activision: hold my beer

THQ: hold my brandy

Capcom and Konami: hold our sake

Ubisoft: hold my bordeaux wine

Shitty indie devs: hold our craft beer

Paradox Interactive and CD Project RED: Whoooo, free drinks!

The Boss. It’s rare that I cry when finishing the villain

Luca Blight is always my go-to answer for this question.  I think part of that is that he went out like a bloody star.  I'll never forget his last stand:

"It took hundreds to kill me but I killed humans by the thousands!!!! Look at me!!!! I am sublime!!!! I am the true face of evil!!!!"

One villain I never really got the appeal of was Vaas from Far Cry 3.  He was just a minor warlord who didn't really stand out to me.  

Really, the storytelling in video games usually has to be so basic that it's hard to mold a great villain from scratch.  You look at absolutely amazing villains, like Johan from Monster, and it's obvious how hard it would be to incorporate that much development in an interactive medium.  

Ygdrassil from Tales of Symphonia, a perfect balance of an imposing, poweful character with fleshed out tragedy and sympathetic backstory and a fantastic parallel to Lloyd the main hero.

Magolor from Kirby's Return to Dreamland was really memorable in execution, from both story and gameplay, also the Hyness + Void Termina combo in Star Allies, Hyness just for his insane personality that only gets more tragic the more you uncover of his past and Void Termina marks Kirby's finest moment, for both its origin and entire build up of decades of the series.

Kefka is really good.

Bowser in Odyssey and Dream Team is amazingly satisfying to fight, his character and plans are very well done in these games. Dimentio from Super Paper Mario and Princess Shroob from Partners in Time are great as well.

Vergil in Devil May Cry 3 is absolutely legendary, as a rival in an action title and from the whole story development.

Bowser, he’s the posterboy for video game villains after all.

S- and Z-blocks in Tetris.