Ooh, neat topic. I'll take:
Shadow, JA2. Coupled with my custom merc, Nailer, the two could rooftop snipe entire levels with ease.
Magic, JA2. He could open any lock, shot unbearably well, and somehow managed to get the first turn on all those mother ****ing ****suckers who just sat around corners waiting for something to shoot.
Dakkon, PS:T. For the reason already given. Studying with him, finding out his past and yours, was just great. He was also a cool character on his own merit, and he was good in combat.
Nordom, PS:T. He was just a fun concept and I'll liked playing with him in the dialogue.
Morte. PS:T. The part where the cracks disapeared in his head made me weep openly.
Dogmeat, FO. He'd knock a bad guy on his back and chew on his groin while I shot him in the eyes. Best dog ever.
HK-47. He was cool and funny. Incidentally, I got a wierd deja-vu Dakkony feeling when I uncovered the full extent of his history.
Korgan, BG2. He was actually an interesting, believable character in a cast of characters consisting mostly of the mentally handicapped, mentally unstable, and mentally deficient. He was simply a pro.
Viconia, BG2. She was a good healer, had a cool backstory, and made for good dialogue at times like when she served as a guide in the Underdark. The fact that you can show her your dia-log has nothing to do with her making the list.
Deadpool, MUA. Not sure he really counts, but in Marvel UA, he rocks.