The top of a toilet seat isn't that difficult to keep stain-free; give it a few swipes with a disinfectant, and it should be ready for the next use. It's the underside of the seat that can inspire nightmares, particularly around the rubber bumpers and near the hinges. Wooden seats are especially vulnerable to the mold and mineral deposits that cause discoloration. To clean a severely stained toilet seat, first remove the seat.
Where the Sun Don't Shine
Mold grows in dark, moist places, which is a good description of the inside of your toilet when the lid is closed. Bleach kills mold, so spraying the discolored areas on the underside of the toilet seat with a solution of one part bleach and three parts water and scrubbing with an abrasive sponge or toothbrush should clear them up. You'll want to wear rubber gloves when you do this. Commercial toilet bowl cleaners usually include chlorine as a disinfectant, and you can use one of these on the seat, provided you rinse well with water after scrubbing. Both bleach and conventional bowl cleaners quickly handle urine stains as well as mold.
About Those Minerals
If you have hard water, you may find yellow, brown or black mineral discoloration on the seat; the minerals get left behind when moisture condenses on the seat and then evaporates. Bleach won't remove this discoloration, but vinegar or lemon juice will. To give either of these acidic cleaners time to work, make a paste using borax as a thickening agent; spread it on liberally and wait a few hours. When it dries out, simply brush it off, and you should see a noticeable improvement. If not, repeat the procedure. Rinse with plenty of water when the stains are gone.
If your toilet seat has received little care over the years, you may find it easier to take it off and immerse it in a 1-to-3 solution of bleach and water or -- to remove mineral stains -- a 1-to-1 solution of vinegar and water. To do this, reach under the toilet and unscrew the bolts holding the seat to the bowl -- okay, it may be more involved than that. Many manufacturers use metal bolts, and these can corrode. If you can't turn the bolts with a conventional wrench, deep-socket wrench or locking pliers after dousing them with spray lubricant, you may have to drill the bolts to split them open. Never fear: New bolts are easy to find, and they're inexpensive.
Time For a New Seat
If you have to drill the bolts off your toilet seat to clean it because it's severely stained, it may be better to get a new seat rather than try to clean the old one. This is especially true if the seat is made of wood. A good chance exists that the blackening you see is water-damaged wood, and to repair that, you'll have to strip the old finish, bleach the wood and refinish. That's a lot of work to do when you can buy a new seat for about 20 dollars.