Quite a few:
First of all, Collette from Tales of Symphonia. I didn't mind her cliched character, but GOOD LORD THAT VOICE ACTOR MADE ME HATE AS I HAVE NEVER HATED BEFORE. I cheered when she lost her voice.
Yukari in Persona 3. She just got annoying with her... prepiness? I guess?
Pepper in Future Tactics: The Uprising. Never before has a British accent been so grating.
Rikku from FFX. So "genki" it was infuriating, and her voice actor didn't help.
Anise in Tales of the Abyss. Just... urg.
Danette in Soul Nomad and the World Eaters. Although she provided an excellent target for Gig's snark, so I suppose not as extreme as others.
Estelle in Tales of Vesperia. A friend and I took to referring to her as "Other Collette" thanks to those pesky "morals" she seemed to cling to, and her annoying naivete.
Lina in Riveria: The Promised Land, for reasons similar to my hate for Rikku. In addition, she's such obvious loli bait it was painful.
And finally, Enrique from Skies of Arcadia: Legends. He was worthless in combat (except for that ONE MOVE that isn't necessary anyway), annoying in cutscenes, and treated like an important character when he actually did very little except follow Vyse around.