Prefab modules that presume the party will suddenly realize something, or will just automatically go in a specific direction. I'm running a game now, using a lot of pre-fab modules and have found that it's like herding cats when the module presumes "at this point the PC's will realize that their best lead is to go to *blah*" when they've already ruled that out as a trick/trap (and honestly, with the way the modules are written, I agree).
Prefab modules that are so cliche that experienced players can walk right through them. In a prior campaign, when I tried to use prefab modules, but one player had run through so many old Dungeon modules that she could deduce the outcome and all the plot twists less than an hour into the module. A lot of pregen modules are so formulaic I think they take a template and just add new backdrops/NPC's/setting elements.
GM's who have a "Pet" PC. Worse than a Pet NPC, the Pet PC can do no wrong. In one political game I was in once, the Pet PC (PC'ed by the GM's fiancee) knew everone elses plots and plans. If you told the GM what you were doing, she automatically knew what it was and countered it. Trying to counter her plans would be doomed to failure, and if you managed to uncover her secrets, you mysteriously died that night in your sleep. Now, the GM loved Railroading, and I think he used Pet PC's (he's had them in all of his campaigns), to enforce railroading, but it just strikes me as unfair and biased.
GM Favoritism. The GM's got his best friends/lovers and they can do no wrong. They aren't attacked as often by monsters, they randomly get good fortune or favors from NPC's, and miraculously they can play the rare/exotic character types while everyone else plays average characters who get killed off regularly and live to be the side-characters in the story of the favored PC's.
Railroading, everyone else has sounded off for it, but I've got to speak my peace too. When the GM has written the whole plot of the adventure in advance, and nobody can steer it any other way, it's less like playing a tabletop game and more like a low-tech CRPG, or worse yet, watching a movie where you roll dice (in the more extreme cases of railroading).
Wannabe Novels. Some GM's are aspiring writers, and it's pretty obvious they are using their games as a testing ground for their novel characters/plots. Sometimes they even admit they are writing a novella/novel/serial based on the campaign, but they of course edit everything to make the PC's exactly how he wants them (assuming he didn't force it like that up front). I think this is related to railroading.
"Because I'm the GM and I say so". GM's who don't explain their arbitrary rulings. Disallow some spells, feats, classes, sure, but I'd appreciate some words on why. They aren't thematic for the setting, just tell me. There is a storyline reason and you have to find out in game, sure. But when the GM acts like a soveriegn Lord & Master who hands down arbitrary edicts to the lowly players. Gaming isn't feudalism, it's a partnership.
"But the rules say I can." The other side of the coin of "Because I'm the GM". Players who try and cram rules down the GM's throat and assume that because something has been published, it's in the game, and because they meet all the prereqs they can take any feat or class out there. Some things aren't right for all games (but the GM needs to say up front what is or isn't allowed, and preferably give a reason). That and people who try and rules-lawyer the GM in the middle of a fight (especially over little things).
People on either side of the screen who treat Alignment as a straightjacket. "You can't do that, that would be against your alignment", or "I can't do that, it would violate my alignment". Alignment reflects how your character normally acts, normally lawful people do chaotic acts occasionally, chaotic characters can act lawful enough to keep out of trouble most of the time, evil characters aren't beyond an occasional act of charity, and good characters aren't free of vice or sin. Unless you are under alignment restrictions or a code of conduct, play your character as you wish, and let your alignment reflect your actions (if you are under restrictions, play your character, and try and play him within those limits, and your alignment shouldn't matter)
People who try and use Chaotic Neutral (or evil) alignment as a blanket excuse to act however they want (and typically act chaotic evil in the process). Reasons like that are why I don't allow Evil or CN characters in my games.