The current site.py has 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.

Attached is a patch to CVS HEAD that:
(1) Removes the os.path.exists() / os.path.isdir() restrictions
(2) Changes the .pth reader to use addsitedir() (top down) rather than 
sys.path.append()
(3) makepath() uses os.path.expanduser() after the os.path.join().