I vote for no namespace, no prefix, it's difficult enough to organize files for pd, and many prefixes won't work with externals that requires a script, for example if I put my python scripts into extra/python, I'd call the script with [pyext] with a namespace like that [py python/myscript myclass] but obviously it won't work, in fact I'd have to start pd with -path python or put the script into the patch's folder and put no namespace for the script file reconized, same thing with tcl scripts, etc... I'd add that a good taxonomy should take into account any pd and external related files.
Using no namespace, no preffix is what started this whole mess.
Tom