Here's a bit of cutscene from Resident Evil 4 with Ashley Graham
http://www.ebaumsworld.com/video/watch/82174365/And there's the Empire's abuse of Terra in FFIII/FFVI depending on whether you played the SNES version or the GBA version
http://www.ebaumsworld.com/video/watch/81399068/In Yu-Gi-Oh! Worldwide Edition Stairway to the Destined Duel, there's a game event where you're taken to a pyramid and you have to duel against mind-controlled Tea and Joey, in addition to Marik and Odion.
In Megaman Battle Network III (both Blue and White), there's a scenario where Lan and his friends catch Flashman and his operator stealing a program from the school's computers. Flashman uses his Hypno Flash on Lan's friends, causing Dex to think he's a train, Yai to think she's a swan, and Mayl to turn into a mindless zombie.
http://www.youtube.com/watch?v=lG8jfCGjuEMIn Megaman Battle Network V (both versions), pretty much everybody except Lan gets mind-controlled in some way or another over the course of the game.
In Final Fantasy II for the SNES (aka Final Fantasy IV), Kain is repeatedly mind-controlled into betraying the party.
In The Legend of Zelda: A Link to the Past, Aghnim places the palace guards under control to make them hunt down Link and Zelda.
Princess Peach gets possessed by the Shadow Queen in "The Thousand Year Door"
In Super Smash Bros. Meelee, Mewtwo hypnotizes Princess Zelda to fight you until he shows up.
In the American version of Double Dragon III for the NES, Marion is possessed into fighting you as "Queen Noiram."
In the Elven campaign of Heroes of Might and Magic IV, the hero's girl has been kidnapped by his evil rival, who puts her under a mind control spell. The only way to free her from it (even killing the Big Bad won't do it), is to construct the Mirror of True Love. All she has to do is look into it to see her true love's face, and the spell will be broken. However, the Big Bad mentions in a not-so-subtle manner that they have already consummated their "relationship."
Various Jedi Knight games naturally allow you to use the Jedi Mind Trick:)
I'm not sure if this counts, but in Monopoly for the NES, if you had at least 2 human players and only 1 controller, when you hit "select" to go to the in-game menu, it will ask "to whom am I speaking?" and you can change the computer players (such as Carmen and Penelope) from "Computer" to "Human" and make them do whatever you want.