Let's see, most of them have already been listed...
Penny Locking (the best, works flawlessly)
This one is easy and cheap to do. We used pennies because dorm dwellers are broke! Anyway, the easiest way to do it is to buy a claw hammer or a small prybar, either available at WalMart or whatever pretty cheap and extremely reuseable. Dorm room doors ALWAYS open into the room, or else people would hit them when running down the hall. Pry between the door and the doorjam close to where the doorknob latch enters the doorjamb. Get the biggest gap possible and shove a stack of pennies into the gap, filling it as tight as possible. What this does is place enough force against the doorknob latch inside of the doorjam that an EXTREMELY high amount of strength will be needed to turn the doorknob. I've never seen anyone able to do this. It is kind of hard to understand if you haven't done it before, so try this...go to your door and look at how it works. There is the male portion on the door and the female portion in the doorjam. Normally, the doorknob turns easily and the door opens. Now, pull hard on the door (or push, depending on which way it opens) and then turn the knob. It should be harder to turn because the force is causing the male part to be pushed up against the side of the female part with friction being the resistance. The hammer or prybar is also handy when YOU get pennylocked into your room. You can use it to remove the hinge pins on your door to get out. It's either that or tie your bedsheets together and climb out the window (that actually happened with one guy during finals week, but it was only from the 2nd floor).
red cool-aid in the shower head
Pretty self-explanatory, shower heads must be removeable. This is best done in dorms that have "community bathrooms" where the whole wing or floor shares one large bathroom. Unscrew the shower head, pour the cool-aid powder into the inside of the shower head, screw shower head back on.
Trashcan of piss leaned against unsuspecting resident's door
Self-explanatory, takes the cooperation of several friends and the unsuspecting resident must be highly disliked.
Pouring water under door THEN doing the talcum powder trick
Self-explanatory, water can easily be poured under the door using a trashcan or trashcans of water and the cover ripped off of a spiral notebook acting as a "ramp" for the water to run down.
Vaseline on doorknobs and toilet seats
Self-explanatory, use thin films in order to make it unnoticeable.
Saranwrap on the toilet bowl
Easy enough. Lighting must be just right. Also works good for people peeing. It will just run off onto the floor and possibly on their shoes.
Laundry detergent/dish soap/bubble bath in school fountain
Again, self-explanatory. Drawback to this one is the cost of the materials used.
Icy Hot in the crotch of someone's underwear (did this in Marine Corps bootcamp AFTER time spent in the dorms)
Self-explanatory. Helps if the victim lays out his clothes before going to the shower or whatever, or takes them into the bathroom with him.
Filled an ENTIRE dorm room (to the ceiling, via a removeable vent in the door) with balls of wadded up newspaper that was collected for recycling (requires an entire weekend)
This one is hard to do. Takes a lot of manpower and a lot of time. Victim needs to go home for the weekend or something along those lines. Materials must be gathered over a long period of time. The good thing about the materials that makes gathering easier is that these schools have daily university newspapers that are free for the taking and usually dropped off in stacks in each dorm and other buildings across campus.
Tie doorknobs together
Take a long rope and go down one side of the hall as far as the rope allows, tying all of the doorknobs together as tightly as possible. This will prevent them from being able to open the door and affects many more people than just pennylocking one door, but it is of course more noticeable to some "good Samaritan" walking down the hall. Sometimes, people can really screw up a good prank.
Other things not really considered pranks were things such as fruit from the cafeteria and waterballoons launched out of 3-man slingshots into parking lots, against the sides of buildings, etc., drawing on passed-out drunks with permanent markers, shaving cream, and toothpaste (this happened to me as well, so it's ok to do to others), shaking up and throwing 2-liter bottles of Sprite or any other favorite carbonated drink from a top floor window onto a sidewalk (sets of stairs are better because of the stair edges), and a few other things I'm sure we did that I can't recall right now.
Have fun and be safe.