I've been playing with a similar structure for another purpose, but 
have been wondering what the best way to perform a search under a 
given point in the tree is.  I can see a few:
1)  Use Lucene and on creation of a site, add all of it's parent sites 
as metadata to lucene.  Unfortunately, this means moving all the 
metadata when a node or site is relocacted, including adjusting all 
child nodes when moving a mid-level node.  Additionally, it requires a 
series of traversal steps to find all of the parents, and this may be 
a series of queries to the database.
2)  Store as metadata on the object/table the parent sites of each 
node.  Again, on moving nodes, you have to readjust your metadata.
3)  Perform all of your searches by selecting the node under which you 
want to see the results and traverse.  Unfortunately here, it's harder 
to do a query that returns these results and includes an "and".  
e.g. "All sites under site X, and with characteristic Y.
4)  Limit the heirarchy to one level deep, and thus every child has 
only one ancestor.  While this is restrictive, for some functions, it 
is suitable.

Others?