Just try to not produce conflicts for people when updating. And keep subversion history, obviously. I'm not sure if moving in two steps would be good (svn mv, but first commit the additions, then the deletes), as it would allow for an intermediate step, where you could move things in that revision.
The are files not-handled by subversion, such as extenals (WikiWord folder will be a problem) or modified ones. For instance, if you moved pngds, I would get an error because folder pngds cannot be deleted (I have the three binaries there, thus it would be non-empty).
Maybe post a plan of the moves before? I'm not sure what to do with some projects. When is a project worth enough to be on trunk and when it needs to go under tools ?