I just add a very small amount of bleach to a full water bottle; let it sit for a bit; shake the heck out of it; and rinse it out very well.

NOTE: IF YOU DON'T LIVE ALONE, THEN YOU SHOULD MARK THE BOTTLE IN SOME WAY WHILE IT'S FULL OF THE BLEACH SOLUTION.

EDIT: If you're wondering about the warning -I let a bottle full of the bleach solution sit overnight. I was running late the next morning, and my girlfriend was helping me get out the door. She handed me my bottle of bleach water, and I didn't notice it until I was on the road. Luckily, I realized what happened just as I was bringing the bottle to my lips.

On second thought, it might be best to immediately shake it and rinse it.