A few weeks ago I put together a patch to site.py for Python 2.5 http://python.org/sf/1174614 that solves three major deficiencies:
(1) All site dirs must exist on the filesystem: Since PEP 302 (New Import Hooks) was adopted, this is not necessarily true. sys.meta_path and sys.path_hooks can have valid uses for non- existent paths. Even the standard zipimport hook supports in-zip- file paths (i.e. foo.zip/bar).
(2) The directories added to sys.path by .pth files are not scanned for further .pth files. If they were, you could make life much easier on developers and users of multi-user systems. For example, it would be possible for an administrator to drop in a .pth file into the system-wide site-packages to allow users to have their own local site-packages folder. Currently, you could try this, but it wouldn't work because many packages such as PIL, Numeric, and PyObjC take advantage of .pth files during their installation.
(3) To support the above use case, .pth files should be allowed to use os.path.expanduser(), so you can toss a tilde in front and do the right thing. Currently, the only way to support (2) is to use an ugly "import" pth hook.
So far, it seem that only JvR has reviewed the patch, and recommends apply. I'd like to apply it, but it should probably have a bit more review first. If no negative comments show up for a week or two, I'll assume that people like it or don't care, and apply.