A few drops of bleach, then fill the bottle with water and allow to sit. I think this was mentioned before, but it does work. Be sure to rinse well to get out the bleachy taste. I also like the idea of storing them in the freezer, once they are clean.

Some bottles deserve to be tossed after so many uses, but there are some "special" ones you might like to have around for awhile, so keeping them sanitary is one way to do it.