I'm sure you've already done it, but if not here's a pair of suggestions:

1) In hypershade, Edit->Delete Unused Nodes

or

2) In the hypergraph, hit the Input Connections button (as in the one to the left of the icon with a book and a red + symbol)
Then go through and delete any nodes that you know shouldn't be there.


3) Failing that, as a last resort I'd just save as a .ma and then go hunting through the file for anything that's not meant to be there. I'd just copy the file, do a search and replace (replacing found text with a single space) for everything I know I need. After I'd done that, I'd be left with a file full of spaces and nodes that (a)shouldn't be there, or (b) I'm yet to discover more about.

I've had a problem with screwed-up scenes that stop responding correctly, usually when I convert from polys to subds and then rather than converting back again, I hit undo. This appears to create another instance(a copy, not a true instance) of the geometry, that is not selectable seperately to the original.

Some of the poly ops stop working at this point and the filesize doubles. I've found trick #2 to fix anything remaining after #1.

Simon