I had a plague of fruit flies this year, too (and regular flies earlier in the summer). Very annoying, to say the least, and of course you can't spray when you've got a rabbit living there (or in the kitchen in general).
The most effective thing I found was a variant on flypaper which is a transparent plastic, about 2"x4", gummed all over one side with a thin sticky strip on the other side. I got them at the local Agway. You put it on the bottom edge of a window pane where the flies tend to congregate, and it works great. I put some in the living room window, which gets the morning sun, and within a few days the strips were covered in flies and the problem was basically solved. Once you break the breeding cycle, unless there's an outside source of flies, you're OK.
I also put one over a shallow dish with about 1/8" of graprefruit juice in the dish - the fruit flies were attracted by the juice, and many of the ones which didn't just drown in the juice got stuck to the plastic strip when they flew up from the surface.