On the plus side, most schools cover your flights, housing, and food if you get invited to the interviews. Med school is not so kind; I've heard costs upwards of $2k for the entire application process.
One of my colleagues joked "Sure, it sucks, but it's negligible compared to the costs of the impending schooling :D".
The way I understand it is that it's fairly well adjusted for the cost of living wherever the school's located. The stipend from UCLA is around 35k, but Dartmouth's is only ~25k. So yeah, around $10k variance. I'm going to accrue some dept, because Ramen noodles are going to get really boring after a couple months. That's ok though, this is an investment in future salaries. What's ironic is that I'll be making far less during my post-doc than I am right now, but things should rapidly improve from there.
Honestly, I think it's just cultural... a nationwide pact between universities to milk every last drop of cheap labor out of soon-to-be ex-students. If I ever hear otherwise, I'll try to remember to let you know.