The /usr/bin/open command defaults to using either a Finder creator or the file's extension (if the Creator isn't set in the desktop database) to decide which application to invoke. This can be a pain for files with extensions other than those that are in Project Builder's plist.
Fortunately, open has a -a switch that allows you to specify the application. For example:
open -a /Developer/Applications/Project\ Builder.app somefile.php
will open somefile.php in Project Builder. I do this so often that I have an alias in my .rc file:
alias openpb 'open -a /Developer/Applications/Project\ Builder.app'
One can use a similar trick for opening files in BBEdit (yes, I have an 'openbb' alias as well) or just about any other editor you want to use (so long as the editor responds to the Open AppleEvent).