For bottles that have been sitting in my garage for awhile or are of unknown origin, I soak in a water/bleach solution, rinse thoroughly, then run them through the DW without soap. Bottles I have just emptied, I rinse three times with hot tap water and give them the same DW treatment - skipping the water/bleach step. I've never had a problem from unsanitary bottles.
Some bottles end up with some droplets of water in them, but I just bottle anyway. No problems, so far (knock wood!).