How to clean funky bottles

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I would just throw together a sink full of bleach water, soak them overnight, rinse well, and you are all set.
 
Unscented oxyclean works really well for me, for cleaning the inside of the bottle and also for delabeling. I'll usually let them soak for about 24 hours, after that their in pretty good shape. If they have a bunch of nastiness on the inside of the bottle then you should also use a bottle brush to scrub the inside.
 
Star San is a disinfectant and not known as a cleaner. You gotta clean out the crud first. Soak them in a convectional cleaner first.
 
The only think I would caution about a lengthy soak is particles settling in the bottles and sticking to the sides.

I stripped the labels off about 100 bottles by putting them in the bathtub with oxyclean unscented and peeling/scraping labels off about 10 of them at a time. It took three days. My wife was out of town, so I took my time.

Flash forward to the last batch of beer I bottled. They all looked clean once I rinsed and sanitized. However, some of the glue must've dissolved into the water, which settled on the sides of the bottles on the inside. Once the beer was bottled, I could tell there was "stuff" on the sides of the bottles. Luckily, nothing seemed off or infected. Now, I need to do a second oxyclean soak and maybe get a real bottle washer to spray out the insides.
 
I like to just fill them with oxyclean (just fill the bottles, no soaking) and let them set overnight. If any are really bad I just throw them away and set into a mixed 12 pack until I've emptied enough replacements.
 
+1 on the unscented oxiclean soak. Works like a charm, both for cleaning and for label removing :)
 
Like Jet was saying i only fill the bucket with Oxyclean to the necks. Fill the bottles with Oxyclean so they sit but the water shouldn't be high enough so crap can get into the bottle. This keeps the glue and crud from getting inside the bottle.
 
I would chuck them and buy some beer in bottles you can use for bottling. Of course I have a somewhat steady supply of newish bottles and can be a little picky. I don't bother with bottles that have gunk.

Edit: If you must clean them I agree Oxiclean Free is the way to go.
 
For me, hot oxy-clean free soak overnight, then bottle brush in the cordless drill, then bottle washer blast with super hot tap water, dry overnight, then star-san before bottling. Overkill, maybe, but I had some stuck on Apfelwein yeast in some bottles ruin about half a batch of IPA, so no chances taken now. Every bottle before bottling, no exceptions.

Sanitation, sanitation, sanitation....
 
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