Warm water and a bottle brush is effective, and then rinse the bottle a couple of times. If there aren't any deposits from the chemicals then a couple of rinses should be enough. Remember to give the bottle cap a good rinse too.
Yeah, that's how I started out. Until I learned the trick of taking a small scrap of *whatever* (sponge, scouring pad, etc.) put into bottle, fill bottle for about 10% with water and then shake like a madman. Most of whatever was stuck to the walls of the bottle will rinse away easily after this. You can do the same procedure with a cleaning agent of your choice; it doesn't have to be water. I find this procedure a lot easier and more effective than the 'appropriate' cleaning tool.
Actually my bottle brush has a sponge on the end, but it needs a longer handle.
As a home brewer who occasionally forgets to wash out a bottle after emptying it, I learned that a stubborn deposit in the bottom can easily be removed by adding a small amount of water and a few pieces of pea gravel. It's sort of like doing a wet media blasting.
IMO, you can just rinse them out a few times. No need to discard them. Especially if you are putting stop and fixer in them. Developer gets carried over into stop and fixer all the time, so if you put stop/fixer in a bottle that used to have developer, it shouldn't cause a problem. Where one needs to be a little more careful is putting developer into a bottle that used to have stop or fixer, since remnant acid could inactivate the developer. However, rinsing several times should dilute any remnants to insignificance, unless you have a lot of precipitate in the bottles.
For plastic trays and glass bottles I use diluted household bleach.
Leave to soak overnight and give a good wash out before use.
If storing empty glass bottles for some time I use the the homebrewing technique of putting an inch of DILUTED Sodium metabisulphate in each bottle before capping. Obviously they need a good rinse immediately before use.
The Sodium met. stops mold growing in the damp bottles. Any homebrewing site will give you the correct rate of dilution. I usually mix a full teaspoon with a pint of COLD water. Do not use hot water as the fumes will not be nice.
Have a care though not to sniff the bottles as it is irritant, but not that bad as it is allowed in foodstuffs.
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