I usually just soak them in Oxiclean Free in a bucket overnight once 4-6 are dirty (or PBW cleaner when I had it around when I would homebrew). You can also just put the Oxiclean in the bottles and let them sit overnight.

I also have a narrow bottle brush that I'll use that fits in there, but honestly the oxiclean basically cleans everything, even crusted junk, with an overnight soak. Then I just rinse them thoroughly.

I've also added coarse salt and rubbing alcohol and shaken the shit out of them then put them in the dishwasher for a box of like 30 of them that I bought at a garage sale for $1 (I don't think the dude ever even rinsed them after drinking the beer), but that's before I discovered how well oxiclean soak works.

If they're not particularly crusty, I'll just add a little dish soap and hot water and shake. Cleans them fine for me for me for the ones that get used more quickly/regularly.