Hi zChris,
welcome to the project!
jAmiga should be buildable with GCC for OS3. I have however not been able to try it myself. I haver tried getting a cross-compiler environment for Linux functioning, but have focused on OS4.
The README (http://code.google.com/p/jamiga2/source/browse/trunk/jamiga/README) mentions how it should be done. There is a Makefile in the root-dir, that I think does *not* work yet, so you have to manually CD to each java-#? dir according to the readme.
Each Makefile includes the CrossCompile.mk (for main exec under src/) and LibCrossCompile.mk (for libraries under each java-#? dir), any changes needed for different compilers should go there. If you make changes, please supply them so I can update the SVN.
In what kind of environment are you trying to build it? OS3 on WinUAE and some Geek gadget-install, or some cross-compiler setup?
/Joakim