Resident Evil 4's main badguy Saddler takes direct control out of the barely legal president's daughter. Her head slumps, eyes change color and she does the no-speaking slow walk to his side. If the RE franchise wasn't so ---squicky with the biohazards--- I'd probably enjoy that more than I did. As it stands.... 6 out of 10.
Resident Evil 5 has Jill Valentine as Wesker's brainwashed slave until the gem on her chest is shot off. She exhibits no personality while in this state.
Persona 3 has the Lover's event where the main character is being seduced by the enemy shadow into making love with a female character who is in the shower. His head is foggy and words are pounding into his brain. You cannot do anything but overcome them, though.
Also Aigis is reprogrammed and used to fight the team during the final months. The final sprite on the second row shows her in "Mind Control" state
www.spriters-resource.com/resources/sheets/23/24742.pngI have always had an affinity for Rinoa being totally and utterly dominated by Edea in the final scene of Disc 1 Final Fantasy VIII. She tries to approach the sorceress and defeat her single handedly. Without looking she picks her up in the air, takes full control of her mind and puppets her to walk on stage with her and be sacrificed for the crowd. During the scene she is swaying heavily and can barely keep her eyes open... I will admit, when I was young, that 4 seconds of FMV drove me far more crazy than it should have. Good graphics were hard to find back then.
Tales of Vesperia has Estelle kidnapped by the big bad and used as a weapon against you, so you get to fight her while she has delicious Fujishima artwork mind control eyes... aaah, Fujishima... *wistful sigh*
Collette and Presea gets those same eyes in Tales of Symphonia but it's less mind control and more "her soul is being hollowed out and she is becoming an unfeeling human puppet.
Lunar: Silver Star has a REALLY good example. The main love interest, Luna, is kidnapped by the big bad because she is the living avatar of the Goddess. He spends the entire time you're on adventure brainwashing her until you come across a village which has been plagued. When you reach the end of the dungeon you see her, empty eyed and singing a song that harms all who hear it.
www.spriters-resource.com/resources/sheets/55/58081.png - Sprites
Then at the end of the game he has summoned the Goddess back into her body and uses her to purge the Earth and start anew. In this form she clings to him like her were her pimp and it's freaking delicious.
Malesub fans of course have Cloud being Sephiroth's puppet throughout FFVII (and I know malesub is a rarity, but I am surprised there is less of that in the community) and the first two Arkham games have Poison Ivy's mind controlled minions all singing songs of sweet devotion to her during her boss battles.
I'm sure I'll come up with more soon, those were the ones that sprung to mind right away.