In older versions of Mac OS X, you could set your PATH variable in terminal by adding to your .profile in your home directory. Recently, a bunch of my scripts started to fail because I use a lot of tools that are located in /opt/local/bin and /opt/local/sbin, and those paths were no longer in my PATH environment variable. As of the latest updates to OS X 10.8.3 (Build 12D78), Terminal.app no longer seems to parse .profile when it starts up. What works, now, is to edit "/etc/paths".
I just tested it, and it works.