Toilet paper origami. It's difficult at first, but well worth the time spent on it.
Contemplate the meaningless of life, and some things that you can do to make it a bit better.
Eat bath beads and see which tastes the worst, or how many you can eat before puking.
Bring in food coloring and dye the toilet water red. If you live with others, this may give them cause for great concern. Do not use blue or green as it may stain the toilet, unless of course you don't care about that.
Strip naked and start inspecting your body for strange bumps.
Bring in a book and read a chapter each time you're in there. If you're not in there long enough to get through a chapter, eat more salads and fruit, or learn to read faster.
Determine once and for all if Pluto is actually a planet or not to YOU. Do not tell anyone what you decide, as they will take credit for your ideas.
Close your eyes and see if you can feel your insides moving as you're going to the bathroom.
Think about what you would do if the power suddenly went out and left you alone in the dark. ARE you alone?
Try talking to others outside the bathroom from in the bathroom. Tell them useless information such as what meal you're shitting out. (Note: Not only is this horribly annoying to others, but it's insanely rude. Do not be surprised if you get your ass kicked once leaving the bathroom.)
Bring in chalk and use it to make your own primitive drawings on the walls.
Try to think of a different shape for toilets to be made, and different ways people could sit on them.
Decide if you will leave the toilet seat up, and then argue with someone who complains. Practice saying "It takes more time to bitch about it than to just put it down." and "If you don't look before you sit down, you deserve whatever happens to your ass."
See how hard you can pull on the shower curtain or towel rack until it comes down (if you can reach it from where you're sitting. If not, try to throw things at it).
Throw toilet paper wads at the wall and see how many stick.
Try hovering above the seat and see if you can still get it all in the bowl.
Dump all the shampoo in the toilet before you flush it.
Carve up the soap into interesting shapes.
Pretend you're on a rollercoaster; lift up your legs, make rollercoaster noises and scream.
Soak the toilet paper in the water and put it back on the holder.
See what you can kick while sitting there.
Rip out every other page from any magazine or book nearby and put together your own magazine with them. If it turns out badly, use it as toilet paper.
Pick your nose and leave it on the toilet paper for the next person.
Fill the garbage pail with water.
Bring in your cell phone to talk to others. Inform them that you're in the bathroom.
Cut all the bristles off the toothbrushes. Pile up the cut bits into a pile and then blow on them.
Fill the liquid soap container with water.
Envision that below you, in the bowl, an evil creature/snake/whatever is just about to attack your ass and see if you can freak yourself out.
Hide the lid off the top of the tank.
See how high can you stack the extra toilet paper rolls.
Write messages on the empty toilet paper rolls to aliens or others who use the bathroom.
Dump out the garbage and see what sort of nasty things you or a roommate/family member has been up to.
Imagine what sort of movie/book would have a shot/scene with a character sitting there like you are.
Have a guestbook for visitors to sign while in your bathroom. Go over this while you're in there and make sure to sign it each time you're in there.
Try to memorize articles or paragraphs from a magazine or book. When this fails to impress your friends and family, memorize a book on how to fake your own death but still collect insurance money.
See if you can pull the shit out of your ass.
Write bad poetry on the walls.
Write graffiti about yourself on the walls.