Howdy and a belated welcome to the forum, JTH (we musta missed the fact that your "Pimp My Barge" post was your first).
Organic material that does not need excavated to build the pond can be left in place for the most part. Much of it will be beneficial in one way or another.
-trees, stumps,and logs will provide structure/cover for fish.
-grass and soft, low forbs will provide a ready substrate for macrophytes (tiny living things fish eat) to grow and live on.
-Ground cover will help prevent erosion within the basin as the pond fills and keep the water in the new pond somewhat clearer at first.
Some possible disadvantages might be:
-green trees and stumps less than a few months dead when the pond fills may leach tannin into the water in objectionable amounts - this is most worrisome with some species of oak.
-some kinds of plants might snag lures badly - briars, perhaps?
I suggest you take a look at the
structure thread in the archives which may give you ideas about how trees, etc. can be useful.