I have started making an object oriented PHP interface to PCB files.  It's not 100% complete yet (no netlist or anything yet), but it allows the manipulation of PCB files in a nice clean object oriented fashion.

I have a little PHP script to go along with it which allows you to globally set all your silk widths to the same size (very useful for pre-press), split polygons off on to a separate layer (to remove your ground planes temporarily so you can see what you're doing), merge two layers together, etc.

It's at https://sourceforge.net/projects/phppcb if you're interested.