The site package reads .pth files and inserts directories listed there in sys.path. However it only scans lib directories ( lib/python2.4/site-packages/ and lib/python/site-python/ on UNIX) starting with sys.prefix or sys.exec_prefix for these .pth files. Thus if you install a module distribution using the .pth mechanism but passing --prefix=/foo or --home=/bar to setup.py you're in trouble.
Is it such a weird idea to at least scan the directories given in $PYTHONPATH for .pth files? I would even suggest that site just scans the entire sys.path for .pth files, but it might be that I'm overlooking a security issue there (but having an insecure direcotry on sys.path is dangerous anyway and should not happen afaik). I can agree that scanning for a .pth file inside a directory added by a .pth file is rather useless though.
So this leaves me with the idea of filing a bug to change site to scan $PYTHONPATH directories too... If no one stops me I might do that soon.