My son left his Camelbak sitting with water for two weeks before I discovered it.

Bought a bunch of pipe cleaners from Michael's, cut off the hose at the hose barbs on both ends and threaded these pipe cleaners in bunches of three through the hose until I scrubbed it clean. Used more pipe cleaners on the bottom fitting and as much as I could on a mouthpiece. Scrubbed inside of the bladder with a bottle brush and soap. Rinsed. Then filled kitchen sink with diluted bleach and let the whole assembly sit there for a while and rinsed like heck after. Dried bladder and hose and reassembled the hose.

So far the kid is alive and well.

As far as my own water bottles go - I just run them through the dishwasher with lids upside down and mouthpieces open.