I wash my Nalgene bottles in the dish washer. Nalgene's site says it's ok as long as you don't place them near the heating element. (I've never actually worried about where I put them in the dishwasher, and haven't had trouble.)

I have done this with the Lexan version of the 1L widemouth bottles. They've been used to hold water, Gatorade, bug juice, coffee, soup, whatever, and they don't seem to retain any smells/flavors after going through the dishwasher.

Nalgene also recommends trying soaking in warm water and lemon, water and baking soda, and they even suggested you could put a charcoal briquette wrapped in newspaper into the bottle, seal it up for a few days, and then remove it and clean with hot soapy water.