I feel for you, man! Until last summer I thought those damn things were cute. Well, ok they are cute, but they're also a major PITA! Last spring (2014), I noticed a bunch of holes in my backyard. No dirt piles, just tunnels. I couldn't figure out what kind of critter had made them. One day, I heard one hell of a racket and looked out of my window to see a chipmunk getting out of one of my walls and onto my roof, where the addition is joined to my home. He got into the wall from the crawlspace underneath. I had to get into the wall and replace the fibreglass insulation that the little bugger tore out. The I closed off acess at both ends using wire mesh. They're still getting into my crawlspace, but at least they can't climb up in to the wall anymore.
I've been dealing with the little *^%#$@s ever since. Using peanut butter and sunflower seeds as bait, I managed to catch four of them in a live trap that one neighbor was nice enough to loan to me. One of them, however, must have been trapped before by someone, because it will not go in the trap. So, I made a wooden box with a rat trap in it and, you guessed it, it won't go in there either.
We used to have a cat and she managed to catch at least one of them once. The neighbors cats come in my yard and do a good job of keeping the mice under control, but they don't even try to catch the chipmunks. There are hawks around too, but I think the chipmunks far out number the hawks.
The other annoying pests around here are moles. They tunnel all over the place and leave little black dirt hills, but they're easier to trap than chipmunks. One of them chewed through my phone/internet cable a couple of years ago while it was tunneling.