For some reason, $uname -m returns "i386," even on x86_64 Macs. In order to build an x86_64 binary of the JOCL JNIlib, I had to hard-code the $HP_64 variable in Makefile_common.mk to 'x86_64.' After setting this, compiling, and copying to my java extensions folder, everything worked swimmingly and I'm able to run the samples.
I don't know enough about makefile syntax to know the "right" way to fix this and submit a patch, but I thought it might be useful info for anyone trying to run JOCL on Leopard/Snow Leopard, considering their Java 1.6 JVMs are 64-bit. Also, if anyone does know the "right" way to detect arch on OS X, I'd be glad to learn (I have this problem with building many Java JNIlibs, sadly).