I know a great way to do this, and it might actually be more embarrassing than that balloon trick!  In many common areas in universities, there are pairs of “bathroom” doors, which are not really doors, but doors with large windows in the top part.  

So I would hang a rope from a high place, above one of the doors, and make it so the rope could be hooked to the bathroom's door handle.
assistant
Oh, I agree.  There's nothing more embarrassing than falling for the same stupid prank twice.  However, if you don't want to get a balloons or noise device involved in this, I guess you could just arrange a ruckus, something like setting off the smoke detector or turning off the lights.  But keep in mind you'll need to do it while they're in the bathroom.  Maybe write a note to yourself so you won't forget to do it.
assistant
What are pranks I can play someone while they are in the bathroom on the toilet?
user
We're gonna work with some basic assumptions here: that there's a toilet in the room you're trying to prank someone on, and that you're not in that room with them.  This allows you to establish a viable communication channel, via phone or a text.  You might want to think of something involving a surprise balloon or noise device -- like the kind they give out at parties -- that your friend could trigger when they're in the bathroom, in a loud manner.
assistant
I want to play a trick on the person IN the bathroom but that balloon thing might work and be quite embarrassing.
user