Shang Tsung, MK
Liu Kang, MK
Johnny Sfondi, GG
Eddie, GG
Akuma, SF
Frank Fontaine, BioShock
Solaire, Dark Souls
Midna, LoZ: Twilight Princess
Kerrigan, StarCraft
SHODAN, System Shock
Not sure about my Top 'Tem', but I have a Top Ten, in no order:
1. Dante (Devil May Cry)
2. Master Chief (Halo)
3. Kratos (God of War)
4. Yoshimitsu (Tekken)
5. Sephiroth (FF7)
6. Caius Ballad (FF13-2)
7. Vivi/Zidane/Steiner/Kuja (FF9)
8. Mileena (Mortal Kombat)
9. Captain Price/SOAP (Modern Warfare)
10. Sora/Rikku (Kingdom Hearts)
Dekar (Lufia 2)
Mr. Saturn (Earthbound)
Mario (how can any list not include him?)
The Runaway 5 (Earthbound)
Ghaleon (Lunar)
The Licker (Resident Evil 2)
GLADoS (Portal)
The bounty hunter companion from Mass Efrect 2 (can't remember his name)
This is hard. I know ill forget some. But heres what I know
Lo Wang - Shadow Warrior
Noob Saibot
Psycho - Crysis
Geralt - The Witcher
Nate - The Walking Dead 400 Days
Sonic
Nathan Drake - Uncharted
Cave Johnson - Portal
Vaas - Far Cry 3
Booker DeWitt - Bioshock Infinite
I don't know if they count, but The Narrator from A Stanley Parable would make the list if he does. Also I love Ethan Carter and his story so he'd be at the top if he does, but most kids in video games I probably get extra attached to, Ethan just had the most memorable story.
Looking at that list I'd say my preference is for funny or insane characters, often blended together, who still manage to remain badass. And Booker
1) Lightning - Final Fantasy 13
2) Kitana - Mortal Kombat
3) Fang - Final Fantasy 13
4) Mileena - Mortal Kombat
5) Lulu - Final Fantasy X
6) Nathan Drake - Uncharted (I'd hit it)
7) Chun Li - Street Fighter
8) Raiden - Mortal Kombat
9) Blanka - Street Fighter
10) Ardyn Izunia - Final Fantasy 15 (one of the best villains ever!)