Current PCGen has a memory limit of 128MB min and 256MB max. This no doubt stems from earlier times when memory was scarse.
Howevery, with the new GUI, reports have been coming in that common sources configurations have resulted in OOM errors. An example is PFRPG + APG + a whole adventure path. This happens for me on 64 bits Debian wheezy with Rise of the Runelords.
I propose raising the memorylimit to 256MB and 512MB accordingly. This should be available on most modern systems.
I further propose to make pcgen.sh smarter and let it try to determine how much memory is available on Linux and Mac systems (I'm not much of a Windows developer). The coding should be fairly easy and can have a sane fallback value like 256/512MB.