Spray them out with a garden hose sprayer, scrub with a bottle brush, soak in bleach water, rinse, run them through a sanitize cycle in the dishwasher, soak in star stan before bottling... I've cleaned, sanitized and used many moldy bottles without any problems.
Soak'em in a homer cheapo bucket with 1oz PBW per gallon of water to cover'em 1-2". It should make the mold float overnight. I've done it & it works great.
Soak em in oxyclean for an hour, hot water.
when you are pulling them out, pour out a little oxy and shake the bottle, then dump the rest out.
I usually put them in the dishwasher in a sanitize cycle afterwards.
i soaked them in bleach water over nite and then santized them. i had beer in them before and for got to rinse them out after i used them. i usally rinse them with with bleach and then put them away.
Soak em in oxyclean, run em through the dishwasher. Been doing this same procedure for a year and never had a problem. Some of the bottles I soaked dried before they got to the dishwasher. Considering I can't tell which ones they were, I don't think it affected the beer much.
I just ran into this last brew day. My buddy came over to watch/help for the first time. He showed up with a case of empties and almost all of them had mold in them from not getting rinsed. We soaked in sun cleaner and hot water and the mold floated out of the bottles in a few minutes. I checked every one while rinsing and they all looked clean as new. He learned quite a bit that day, first being rinse out your bottles right away.