Each and every time I place Tupperware or other plastic food storage containers in the dishwasher, I am met with disastrous results. Consequently, I have taken to hand washing all of my containers, even the higher quality ones that are made from hard plastic and resist stains.
The main problem with placing plastic food storage containers in the dishwasher is that they warp to the point where you cannot get the lids to secure onto the bottoms. Now, I clean the containers with a mixture of water, vinegar, ammonia and baking soda.
For containers with tough spaghetti sauce stains I use a diluted bleach mixture. Simply mix equal parts of bleach and water and let it sit in the stained storage container. Then, rinse with clean water and dry. My mom swears by fresh lemon juice to rid plastic storage containers of nasty smells and unsightly food stains, but she dries them outside in the Hawaiian sun, which is not an option for me during winters in Wisconsin.
If you prefer sticking with commercial cleaners, then try OxiClean, Soft Scrub or Cascade Plastic Booster. Just be sure to thoroughly rinse the plastic containers after cleaning them with the commercial products as they contain chemicals that should never be ingested.
Of course, the best way to keep your containers stain-free is to wash them regularly and not let food sit in them for weeks on end, so it gets to a point where mold is a factor. It also helps if you refrain from storing acidic foods such as tomatoes in plastic containers. I also found that placing leftovers that contain a lot of food coloring is not a good idea, especially if the container gets looked over and the items remain in the back of your refrigerator for days.
One final tip: Some manufacturers of plastic food storage containers maintain that their products are dishwasher safe provided they are placed on the top rack of the appliance. I have yet to find a plastic container that has fared well in the dishwasher–even when placed on the top rack. Have you?