I only drink water (no sugary drinks that molds like), and I find that if I rinse them out right away after a ride, and put them in the dishwasher, they are fine.

I think the same would work for water bottles with sugary drinks--just rinse thoroughly as soon as possible, and put them in the dishwasher. If you don't have a dishwasher, getting one of those bottle brushes might work well.