I've produced a .tex file using the pstricks package for figures and the Times font (via the mathptmx package). When the arXiv compiles this to a .pdf file it doesn't seem to have the necessary fonts ...
My thesis currently has a few PSTricks and TikZ pictures. It takes a while to compile over here Scott says he has some scripts to automate externalising TikZ pictures. I'm looking ideally for ...