One secondary goal was to be able to get PCGen characters into MapTool and I found that InitiativeTool now has an export token function in the file menu that does exactly that, fantastic!
This will likely be framework-dependent since much of the combat tracking stuff (hps, etc) won't necessarily be stored the same way by all frameworks. But again, some templates for each framework would be doable; and honestly, once the data is in InitTool it's really not necessary for the PCGen folks to continue trying to push the data around (except perhaps as a curiosity!).
PCGen has quite a bit of data that could probably be transformed without much effort into files usable by the Tools. I'm sure we have some synergies there.
Did PCGen ever transition to XML data files? I signed up on the Y! group (was it d20xmlsrd?) that was discussing how to do it and I believe PCGen was the focus of that effort... Last I looked I still saw mention of LST files though.
PCGen has just recently completed coding the Pathfinder Bestiary so it's possible we could help round out that game setting file by providing the Bestiary lookup tables.
I'd love to have a way to automatically convert that data into tokens for my ongoing PF campaign. Right now I have a statblock parser built using regular expressions that can extract fields understood by the framework and insert them into the token. This makes it pretty easy to copy/paste from the module PDF. But there is still tweaking to do so having a pre-built (and pre-tweaked!) monster dbase would be a huge benefit for me.