I'm using Fink as the package manager for unix/linux stuff here as it's what I'm used to using from years ago, and it seems okay, excerpt on Mac OS X 10.6 they don't have the binaries pre-built yet I guess. So I'm compiling all kinds of stuff from scratch.
So here's a partial listing of the programs missing or seriously outdated on the default Mac install that I got through Fink. Some of them are a little oudated in Fink too though, and installing these will install a slew of other useful things along with it.
Also, I needed LaTeX. It's best to get that through MacTex though (don't bother with the i-Installer stuff you might find elsewhere).