1) Anything that pops up incessantly when you're wandering around a particular route looking for a certain Pokemon.
Examples: Rattata, Pidgey, Spearow, Oddish, Bellsprout, Caterpie, Weedle, Zubat, Zigzagoon, Wurmple, Poochyena, Tentacool, Geodude - and presumably a big pile of Diamond/Pearl/Platinum ones as well (haven't played those).
FUCK OFF. I JUST WANT A {insert Pokemon name here}. LEAVE ME ALONE.
2) The legendaries that run around the region. Forcing you to wander in and out of routes burning money on Repels for HOURS. Even worse if it pops up when you're not actually looking for it (and therefore aren't prepared to inflict some status/False Swipe it to hell), and for whatever reason you've already used your Master Ball.
LATIAS, I WILL FIND YOU IF IT'S THE LAST THING I DO.
3) It's already been said, but the abomination that is Luvdisc. One particular double battle in Emerald is you against a "young couple" both with nothing but those...things.
Aaaagggghhhh.