I have edited an old version of noggit so that I can edit the terrain height (haven't fixed other things such as changing textures yet), save the file back into the MPQ, and update the signature file.
I have also coded a loader that allows me to load WoW with the edited signaturefile. The end result is that I can easily edit the terrain without having to mess around with patch mpqs (do they even work still?).
I have not tried this out on a live server yet, so I don't know if it is useful for that.
I can create a program that will let you place edited files into the MPQs and load them in WoW if that would be useful.