I see there are a few package managers for the Mac from this question.
Apple / Mac OS X - Is there a Package Manager like Linux
It looks like Homebrew is pretty good but I see it wants to change permissions on many system directories. I occasionally will find and fix permissions with Disk Utility and if I use Homebrew that could be a problem. I also question if changing these permissions could represent a security problem. Key directories being group writable is definitely a concern. I prefer to keep things owned by root:wheel instead of changing the group to admin and making it writable which opens up all sorts of issues to any user account which is a member of admin, like my account.
Should I just use MacPorts or Fink? (I see finkproject.org is not online ATM.)
/usr/localon OS X by default, so it depends on your POV if you consider that a "system directory". Closing this question as it's polling for opinion. – Daniel Beck♦ May 3 at 12:49