you could do it with the GD. but they may take quite a bit of coding.
you could also do it with a text based ray tracer program. all the names of those have just dropped from my mind. it would probably be a bit slow.
getting php to create VRML is once of the quickest methods and it looks great. ive done a few graphs using this method.
wildtangents plugin can be programmed from javascript. Youd just need your php to create/alter the javascript.
that should get u started 🙂