Psycho Mantis from MGS1 has a 2nd person perspective, if you press triangle.
One of the bosses from LoZ: Phantom Hourglass also lets you look at Link from the boss' eyes.
Battletoads, like said above.
Turtles in Time (SNES) has the Technodrome boss, which is Shredder looking at the Turtles. You have to throw enemies at the screen to damage him.
There's also the old Sandlot games for the PS2 (Robot Alchemic Drive, Remote Control Dandy SF), where you control various giant robots. You play as a character, and once you position yourself, you use a Remote Control to control the robot. Your character is still there, and you see the battle from his perspective, but you're controlling the robot.