As a point of contrast - I've been using OS X for about 8 weeks and I had some problems when first installing Homebrew (I do not remember the specifics, but I seem to recall some issues with installing iPython and the modules I wanted to use) - and since giving MacPorts a try I've really had no issues with it.
My only advice on MacPorts is to always do a dry-run before installing packages (port -y install), to see what dependencies will be dragged in - installing num.py wanted to re-compile a numerical computing package from scratch which I had to kill after a few hours of compilation (with no visible progress on the command line).
My only advice on MacPorts is to always do a dry-run before installing packages (port -y install), to see what dependencies will be dragged in - installing num.py wanted to re-compile a numerical computing package from scratch which I had to kill after a few hours of compilation (with no visible progress on the command line).