I haven't had to sleep in a bunk bed for a long, long time. My head is in pain just thinking about it though.
If it comes up (for example if you haven't gone to college yet) I found that making a custom loft is the way to go. There will likely be some local companies/contractors used to making custom lofts because of all the different sorts of dorm rooms. They shouldn't have much trouble getting a comfortable bed up in the air.