I used Fink and then Macports. Both were miserable. They did a terrible job with dependencies and many common things (MySql, memecache, ..) either weren't in them or wouldn't install properly. Homebrew concerned me because it defaults to using the base libraries installed by OS X.

That's really the core problem; on linux, all of the software on my machine is from the open source ecosystem and it tends to follow the unix patterns and work well together. On OS X, it was a mix of open source and what comes out of Jobs' Garden. It also meant that ports to OS X package systems were always behind linux.