I'm here more as a reader than as a writer. I was just reminded of this account's existence, actually. For anyone that actually remembers my old fic... I'll find a way to get you a copy if you really want it. I feel too embarrassed to keep it up.
My biggest pet peeve, is perhaps exemplified in the the Ron/Hermione pairing from Harry Potter. You have an intelligent, likeable, female character... And then you pair her off with the dumb comic relief? Actually, this is far more common than you might think.
My second pet peeve, I guess would be called the Shounen Ball. It's basically how the main character is in any shounen anime or manga. His deepest motivation is to protect everyone. He spends all his time doing training from hell. He refuses to kill, even when his opponent will kill again. He is frequently Lawful Stupid in alignment. Dishonorable mention goes to Holly Evans and the Spiral Path.
A third is complexity addiction. Authors use it as a substitute for intelligent villains. These supposed geniuses come up with plots that have extra failure points, and then act shocked when things don't work. Dishonorable mention goes to Partially Kissed Hero.
I don't like femslash. Not so much because I find it inherently bad... It's just that it's typically poorly written smut, when I want a plot.
I also dislike harems or /multi pairings. Mostly for the same reasons as femslash, except with less defined characters.
I hate stupid characters. They can be a useful plot device, but remember Bruce's Law: Any story about Good Guys vs. Bad Guys can only be as smart as your baddest dude. If you don't have smart villains, your plot will be stupid.