You can pretty much get PCGen to do anything you want with a bit of ingenuity.
Classes, feats, skills, equipment are all stored in text files that you can easily add to and manipulate. You can even get it to support non-standard d20 ideas like Monte Cook's skill group idea with a bit of work.
The output sheets are XML based, so with a bit of playing around you can make your own and add whatever fields you like.
You just need to tinker with it - and to not be afraid to do so. I recommend installing two copies of it, one backup with original files, and then one you play with. That way, if you do screw it up you can easily go back to the working version's files.
The Yahoo Group is amazing by the way! The team always is lurking around there and always are quick to help you with problems.