No contrib directory: As stated, make/Cmake is not going to be the "only way" of making the library available. Not everyone has the luxury of automated downloads etc, nor is it desirable. I think the benefit of inclusion outweighs the space saving. Contrib also serves a purpose as for general "stuff" related to Box2D, but not an example or meriting library status.
I noticed that box2d uses a modified version of glui, which of course cannot be discarded since it would break the build on any
So removing Contrib is definitely out of the question.
Instead, i created a new Contrib under Examples/TestBed which hold the library dependencies for the TestBed only. This should give clarity to what belongs where.
Build directory: I don't like the idea of moving stuff to the root directory, it'll get pretty cluttered that way (particularly as VS at least autogenerates a dozen files or so next to the .sln file). Separate folders also makes it clear that this is a varying list. I'm almost inclined to suggest going in the opposite direction, and moving the makefile into the build directory instead. Certainly, by all accounts Source/makefile is a very confusing location. If you want to rename it, I'm open to suggestions.
I've configured a VS9 project to but all output in /Output/<project>, the sollution is in the root, but the project files are in /Build/VS9.
This makes sure that there is minimal clutter in the root, and you still can catch what available builds there are at a glance.
I'm not sure why you want trunk & branch folders. So far, there has been no need to branch the project (though the work on changing the event system could do with it, honestly), but it's surely a developer decision. Unless you want to commit, I cannot see why you cannot create your own branches, or merely have several working directories.
Currently i really feel the need to have the branches directory, since i have to distribute my changes "as a whole" or one giant patch.
There is not nice way for me to integrate any changes that might be done to the library in the future either.