The ones that stick out to me the most are those little repetitive side missions in ME1 and 2, and the completionist in me dreads ever doing them again.
ME1:
The Rogue VI on Luna. I really don't like those rocket drones, and I especially don't like having to shoot through those stupid barriers that just slow me down.
Finding the geth outposts: Motherf**king geth, man. It makes me want to airlock Legion and choose the quarians and be rid of these suckers once and for all. Choosing destroy works just as well though. Helena Blake's mission has this same problem, hunting down mercs in the same generic mines or bases across multiple systems.
Noveria. Oddly enough, I always look forward to going to Noveria, because I love the dialogue that goes on in Port Hanshan. I enjoy having the dialogue options available to go through the entire song and dance with Rafael Vargas, talking to Gianni and so forth. But once I leave the garage to find Liara's cheese-doling mama, it starts to get a little corny. The highlight of that part of the mission is killing that snotty asari scientist, but Benezia is so cheesy it kind of hurts.
I actually kind of enjoy most of Feros. It's just fighting all those stupid creepers that really bugs the sh*t out of me. Flinging the asari clones off the ledges or into walls with my biotics (max push FTW!) more than makes up for it though lol.
Pyjak data module. F*** pyjacks. ME2 did right by me by allowing me to punch and blow up these things.
ME2:
Every Firewalker mission. I hate the Hammerhead, I suppose mostly because of the environments we're stuck in when we use it. Steve Cortez can suck it. I don't care if it's more maneuverable or whatever. I only ever use it to shoot more geth and turrets anyway and I'm just using it to hop around platforms over acid pools or lava. For all the complaints people have with the Mako, there's something satisfying about incinerating mercs from a distance with my main cannon, then rolling up to the front of the base to raid their sorry asses.
That husk mine. The zombie apocalypse is so annoying.
The faulty mech quest line. Because there's nothing I love more than fighting those stupid LOKI mechs.
Excuse me. D-d-d-dangerr-r-r-r-r-r-r-r! [explodes]
Jacob's loyalty mission. Too many of those damn mechs, and annoying baddies. Leaving Jacob's father to be mauled by his crazed crew members makes it worthwhile though.
ME3.
Basically anything with cutscene incompetence, like Thessia. I didn't have so much a problem with Priority Earth, as I was underwhelmed as well as getting slightly depressed, but was never annoyed. Now, Thessia annoyed me a great deal. Funnily enough though, it actually was pretty effective to me in my very first playthrough. It wasn't until my second that I actually looked at it again and thought harder about what happened, and how gypped I felt on a meta level.