See, I don't have a system for using repels is not so concrete.
I keep a bunch of them on hand (Actually, I get loads of them from my PokéWalker), and when I start to FILL WITH RAGE whenever I run into wild Pokémon, it's time to break out the repels.
It doesn't happen much, but in places like caves (ZUBATS ZUBATS EVERYWHERE OH GOD) and some sea routes, they tend to see the light of day.
And when I'm on my way to fight the Big Bad. Then I just don't want to lose my HP or waste my giant stash of Leppa Berries.