One thing I've heard recommend done is taking a piece of aluminum foil and covering the top of the unsanitized (but cleaned) bottle. Try to make the aluminum foil seal around the bottle pretty well. Then bake the bottles at 400F for an hour. The baking will sanitize (and perhaps even sterilize) the bottles and the foil. The foil will then keep out any nasties until you're ready to bottle.
One thing to note, if you haven't sanitized glassware by baking before, is to heat the bottles slowly. Put the bottles in the oven, then set the temperature, and then start the countdown from an hour when the oven reaches 400F. If you just throw the bottles in an already preheated oven (particularly if they're wet) you risk them expanding too quickly and breaking.