They make wood cleaner that should work for the bunkbeds. You should be able to find it just about anywhere - supermarket, hardware store, etc.
Looks like if you clear off some of those papers from the top of your desk, you will have enough room to place the TV there. To organize your shoes, assuming you don't have any shoeboxes or closet space, I would line them up under the bed so that they're out of the way. Throw out the trash lying around and give the carpet a good vacuum and you will be on your way. You definitely should replace that sheet/drape thingy.
Looks like you're only showing us one half of the room. What's going on on the side opposite the bed and couch?
*places fingers against temples*
The bed butts up against the wall, there is a bookshelf there, light colored, taller than the bed with several cubbies
Kidding, I just checked the reflection in the window. There really is no other side of the room in this case, the wood in the picture of the bunk bed is the door and right behind the door is a wall. Between the bed and the wall appears to be a clothes rack and a book shelf
I would nix the couch altogether, its really too big for your room and is probably beyond being reasonably salvageable. Its one thing if the cushions are good and you can slip cover but the cushions on that thing are badly shot, you would pretty much have to replace them, and then having to re-upholster or slip cover on top of it. The only thing you wont be changing is the frame, which is really not much of a desirable frame unless you want to add boosters too it somehow.
Replace it with some chairs. You can either get some butterfly style chairs (might be better for your age), or something bigger, you have the room for it there. Put the tv stand with the tv in the corner and the chairs facing it. You can keep the little side table there as your tv stand, Pick a light (I suggest the black one) and get rid of the other (which looks broken). As Lenohzka suggested, I wouldnt try and save the beds wood look, its very outdated and bad looking. I would sand and paint. She suggest black I think White is also a very good choice considering the construction style of the bed. I would also sand and paint your little tv stand. Those types of dressers/nightstands are a dime a dozen, I see them all the time for really cheap.
I would be more hesitant about painting your computer desk. It could be the lighting but it looks like a nice cherry stain with a good wood grain. But definitely clean up the junk on the desk. I would get rid of the rug too unless its covering a horrible hole in the floor. You have nice windows so frame them instead of covering them. Get two drapes and then set up a rod with lots of extra space on either side so when they are open they dont cover any of the window (this makes your window look bigger as well). Pick a paint color. What you pick may also determine what color you want to paint your furniture. If you go with darker shades I would stick to white, if you get into creams, go black. Anywhere in between just pick whichever you think looks best. Black looks sharper, white make the room look cleaner. Your curtains can also be white or black to go with your furniture.
Frame all your pictures before you put them up. I would suggest doing the opposite of what you paint your furniture (if your furniture is white do black frames, if they are black do white.) You can get frames for $1 at a dollar store as just plain old wood strips nails together with a cheapy ugly picture in them. Rip out the picture, buy fabric paint, use construction paper behind the picture if the frame is too big (it also makes the pictures look very professional).
Get an under the bed shoe orangizer for your shoes and you can attach a strip of fabric to it to make it easy to pull out. I would move the book case to the end of the bed if you get rid of the couch and then hang a few hooks on either side of it for your purse or other items. New comforters wouldnt hurt either but those would be based on wall colors or furniture colors.
Finish up with a bin and recycle tub so you dont get rubbish laying around.