Well, I often get irritated running into wild pokémon, for example in Mount Coronet. However, in LeafGreen, where wild pokémon are actually good (I figured to overcome the problems associated with being underlevelled, i.e. spending two days grinding before the Elite Four, I'd just walk through every patch of grass and capture or defeat every wild pokémon), I've recently found Sandshrew to be awful to face. The only pokémon I have that hits it super-effectively is Clefairy, but Kadabra and Charmeleon can also hit it with special attacks. Because of this, they're all overlevelled, whilst my Pikachu still hasn't hit lv. 20. And since arriving at Vermilion City (I'm now at Rock Tunnel) 90% of my wild encounters have been Sandshrew. So I'm really starting to hate them now.
Outside of that, its usually Golbat. I want to run, but they nearly always force me to stay in, either with Mean Look, or just I can't escape. In the former case they confuse me to death, in the latter they usually poison me somehow and whittle down the health of my lead pokémon (usually one that I'm trying to raise). Removing them in BW was a serious blessing - I didn't realise it until I replayed Diamond though.