I only hate him on the first Toy Story. He’s a jerk to Woody. They needed a character to be entirely against Woody, but I still find him inexcusably annoying for that reason.
I have to say, I don’t find any Pixar characters annoying. I really thought from the first teaser trailer for Nemo that Dory was going to be hugely, majorly, painfully annoying, but she turned out to be adorable! I expected to find Mater annoying, but he was actually pretty funny. And despite my “admired-it-more-than-loved-it” reaction to Wall-E, I don’t dislike or find annoying any of the characters from it.
I will say, however, that my all time least favorite Pixar character is Al from Toy Story 2. I don’t think “annoying” is the right word for him, but he’s IMO completely unappealing. (Usually even the baddies have a certain charm, or amusement factor, or something to make them at least a little bit engaging or interesting.)
I don’t really find any Pixar character annoying. Because if they are, they are annoying… in a good way.
A bug´s life
Heimlic->He was annoying, selfish, only thinking about money and himself.
Molt->He was sooo stupid.
Tuck and Roll->Their jokes were so stupid.
Monsters inc.
Roz->I didn´t like this character. She is too serious and cold. [spoil]Why couldn´t you give more time to Sulley and Boo to say goodbye. [/spoil]
Nemo
Crush and his son= I hate their “yo dude” attitude.
Darla.
Toy Story
Jessie, sometimes.
Cars
Mate= Too dumb and not funny.
The incredibles
Syndrome=So hyperactive and talkative It get me on the nerves.
Wait, are you meaning P.T. Flea? 
That´s right! I couldn´t remember his name 
haha, that’s fine. Hiemlech’s the caterpillar. 
Chick Hicks!!! He was obnoxious. 
I think Chick and P.T. were supposed to be annoying.
MBP13, nice avatar!! 
Thanks! 
I’d say it is Sid from Toy Story who really annoys me the most because I don’t like skull designs (although my Dad and I usually sometimes quote him…)
I also dislike Chef Skinner because he doesn’t really care about the restaurant at all. And Syndrome because his Omnidroid is very destructive. And Chick Hicks because he cheated.
Oh, and Shelby Forthright because he secretly aborted the clean-up mission (which might explain WALL-E’s loneliness).
Man, Chick Hicks is very easily one of my least favorites, he’s just… gross. And not even very compelling of a character.
Can I say I actually find Auto and GO-4 annoying?
Mr. Pricklepants. I don’t think he really did anything in Toy Story 3, but in Toy Story of Terror I really wanted him to get off the screen. He came off like Pixar wasn’t sure if people would notice they were playing with horror tropes and felt the need to make a character to point them out, and the end result just felt really smug.
Emile kind of borderlines this for me, I mean I don’t really feel annoyance but I feel like I should…I guess you could kind of say I know I’d be annoyed if I was Remy. Cause I don’t think the guy does anything but screw things up the whole movie, and he really just acts extremely stupid some times (like when Remy has to shove him out of the way so he doesn’t get stuck in a trap. I mean Remy’s able to recognize it as a trap at a glance but Emile just misses this somehow).