Carpets are notorious for being a haven for dust mites (microscopic bugs that feed on the dead skin cells we constantly shed and whose droppings spur allergies in millions of people). Bare floors, vacuumed and damp-mopped frequently, will help keep your home's dust-mite population down (you can't get rid of them all). If you can't remove all the carpeting in your home, at least opt for bare floors (if necessary, use small, frequently laundered throw rugs) in your bedroom; studies show the bedroom harbors more dust mites than any other room in the home, and you probably spend about a third of your time there every day.
When carpets can't be removed, keeping them as clean as possible will help you breathe a bit easier. But beware: Many vacuums blast small particles of dust back into the air, leaving behind plenty of allergens to keep you sneezing and wheezing. Use a vacuum that has a built-in HEPA filter or attach a filter to the exhaust port of your canister vac (uprights usually don't have an exhaust port). If dust really bothers you and you've got the money, consider investing in an industrial-strength vacuuming system. Some allergists recommend a brand called Nilfisk, which has an excellent filtering system and retails for about $500. To find out whether such products are appropriate for you and where you can purchase filters or special vacuums, talk to your allergist.