Most developers I know who use OSX use brew; fink used to be the big thing, then macports. I know for some certain packages, macports is still preferred.
I don't use any of the extra package managers for OSX. I'd rather let Apple manage the tools available in OSX. If I need to do work where I find the command-line tools on OSX lacking, I'll end up working on a remote server or use a local Linux VM.
I try to not muck around with the base installs too much - it makes it too difficult to migrate between machines.
You should look into homebrew[1] if you haven't already. It installs everything in /usr/local and does not mess with the base install. To migrate between machines you can do something as simple as brew list > brew.txt
