Historically, I've checked the quality of arXiv output by reading the PDF it creates; I learned today that this actually a serious mistake. If you look at the PDF and DVI for my most recent article, you'll see that the PDF looks fine, and the DVI is essentially unusable from a mathematical perspective. The tikz pictures don't come out at all, and there seem to be serious font issues.
I'll note that this file compiles fine as a DVI on my home computer.
What's causing this? Is it a problem a user can fix by include font/style files with his/her upload? is there someone at the arXiv I should be telling to install something? Why is the arXiv less competent than a home installation of MikTeX?
EDIT: So, the take-away seems to be that your DVIs from the arXiv will only look right if you use Computer Modern. Hooray for all math papers looking the same!