Your water bottle is under attack. Bacteria and fungi can find a foothold on nearly anything, and your Nalgenes probably have a distinctive aroma that you just know can't be good. Time to drag them all out for a good cleaning.
Before the Trip
New bottles have a 'new bottle smell'. It's a somewhat plastic taste that can be washed out. Brand new bottles should be washed in warm, soapy water...but be sparing on the soap! You don't want a bubbly residue on your first trip out.
After the Trip
Back to the warm water and a small amount of soap. Swish around. Use a water bottle brush if you used Gatoraid powder or filled your bottle with any kind of food. Store with the lid off so clean air can circulate...bits of moisture will start mold colonies.
After a Month
Okay, you forgot to clean the thing after your last trip and it stinks. You can stick Lexan and #2 Nalgenes in the top rack of your dishwasher, but I've found they don't really get clean this way. I like to use two capfuls of bleach in a filled bottle (use cold water to keep bleach fumes out of your nose). Let sit 20 minutes, rinse well, and air dry.
After a Year
A year? How careless of you. You open your bottle to a REAL foul smell, with fuzzy black organisms growing inside the rim. Still want to drink from it? I suggest finding a new use for this bottle. Clean it up with bleach, then use it to water your houseplants, clean off your paintbrushes, or keep it filled in the freezer to help conserve energy. Then you can stick it in the cooler, for those car camping trips, and it can be a giant ice cube that won't melt. Grab a sharpie and draw a toxic waste icon on the bottle, so nobody drinks from it!

