
As a research biochemist and microbiologist I frequently get asked this question by my fellow mountaineers. It's quite simple really. If you're refilling from streams in the UK/Europe on an overnight camp, it doesn't hurt to throw in a chlorine tablet. That keeps both you and the bottle happy.
As soon as you get home, I agree that a baby bottle steriliser tablet, or an outdoor company proprietory product, should do the job. It's a no brainer. Make sure they are well drained - you can get a drainer from Camelbak. Then store in the freezer.
DO NOT, under any circumstances, use the bottle if it has (green or black) mould growing in it. Contrary to popular belief, it will not give you a dose of penicillin, as that is destroyed in the stomach, and would be too low a dose anyway.
Black mould spores contain quite potently carcinogenic alkaloids - you do not want to ingtest these. So keep them clean. If there is green mould, I'd probably clean the tube out and use, but frankly, if your tube is lined with black mould I'd chuck it and get a replacement part.