I almost forgot Zero from MMX:Command Mission. Incredibly fast and the best damage dealer in the game. Once you unlock his Absolute Zero mode, he can solo most of the game cause he's just ridiculous. Course, Zero is a beast in most Mega Man titles...

Ryogo from Front Mission 3, teamed up the main character, they are unstoppable on his own, he makes you value the power of machine guns since most of his skills and proficiency stems from them. Watching him pull off three special abilities and literally watch him reduce a Wanzer to nothing with just two machine guns is a sight to behold.

Karn from BoF1, he is total bull and the only reason why you would bother with some cast members. For those who don't know, Karn has the ability to fuse with other party members and basically becomes a Swedish Murder Machine, granted he can't fuse with everyone but when he can make the Goldfish guy and Mole kid actually attractive people to bring along, you know something is broken.

I'd also like to second Georg Prime from Suikoden 5 only because I saw him kill a boss, who was at half health and resistant to physical damage, with one attack after something like three parameters all activated at once. He was at low health and activated a move that raises his power, his killer rune activated for a special critical hit, and he went out of turn to do this... It is incredibly rare to see 4 digit damage in Suikoden, at most maybe 1500 but Georg hit for over 5000 with this stunt. There is a damn good reason the game won't allow him to be in your final party until a new game +.

chaos in Xenosaga Episode 1, except for machines (which you rarely fight in this title) and a few Gnosis at the end of the game, chaos is a beast since very few things can resist his innate spirit based attacks, and he gets some truly frightening Tech attacks. chaos has probably been more badly nerfed in later installments than any other character in the series Jr. isn't far behind either since most of his tech attacks hit everything and nothing resists pierce damage.