Well, I tend to use Xfig. It's a GNU X app that has lots of goodies. After you get used to the interface to can rip out flowcharts awfully fast, and they look pretty swish.

There are also some projects on sourceforge, like the kernel map and the newsgroups map. they automatically generate postscript maps of code (or whatever) and once again, look pretty.

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Jeremy
I didn't believe in evil until I dated it.