Looks solid, I can't wait to see some of the runs that take advantage of these tools.
I think putting shared memory in the emulators is a good idea, I've seen no difference in CPU usage (surprisingly) on either operating system. The only problem is that Windows implements it differently than other more POSIX-compliant operating systems so it would be another subsystem that needs to be split up in the codebase.
A linux version of the VBAshm client I slapped together can be perused here: [URL]
http://ikebo.hypermart.net/VisualBoyAdvance-1.7.2shm.tar.bz2[/URL] It stores the shared mem in /dev/shm which can be read simply using standard file i/o. The win32 version is posted above.
It only adds two very tiny modules shm.c and shm.h and replaces a few malloc/free calls with vba_shm_[malloc/free], and modifies the configure script to ensure shm libs are installed.
Trivial changes, and no performance impact, but it may be a headache to sort out by operating system. It would make a great build-time option though.