Here in Aust you can get a product called Milton at the Chemist or supermarket, it is used for sterilising jars etc for jam and for babies bottles so it would definately kill anything bad in a water bottle - I'm sure it would be in the US too.

Sterilising products don't remove the mould or unsightly particles so I would suggest a bottle brush as other have for that.

Also others mentioned clear bottles - they are also better as they are not dark like other bottle therefore the sunlight stops a lot of nasties growing in them. That's why shower mould only grows in the dark corners and bits that don't recieve direct sunlight.