Steps to generate JavaNNS for a Mac with an Intel processor:

0) Folders SNNSv4.3 and JavaNNS are on Desktop, in my case /Users/lc/Desktop, and
Xcode is installed

1) build SNNS
cd ~/Desktop/SNNSv4.3
./configure --build=i686-apple-none
make compile-kernel

2) compile the JavaNNS kernel interface
cd ~/Desktop/JavaNNS/KernelInterface
cc -c -I/System/Library/Frameworks/JavaVM.framework/Headers -I/Developer/SDKs/MacOSX10.6.sdk/System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Headers/ -I/Users/lc/Desktop/SNNSv4.3/kernel/sources/ javanns_KernelInterface.c

cc -dynamiclib -o ~/Desktop/JavaNNS/KernelInterface/precompiled/Mac/libSNNS_jkr.jnilib -lkernel -lfunc -lfl -L. -L/Users/lc/Desktop/SNNSv4.3/kernel/sources/ -framework JavaVM javanns_KernelInterface.o

3) create the jar
cd ~/Desktop/JavaNNS/
ant clean
ant jar

Notes: 
- JavaNNS.jar will be in ~/Desktop/JavaNNS/dist/
  you can move it wherever you want and the first time you run it choose where you want the libSNNS_jkr.jnilib library.  It will put a JavaNNS.properties in your home directory.

- last time I did it my configs were:
  Xcode 3.2.6 (1761)
  java 1.6.0_26
  SNNS 4.3 (this version uses v4.2 user manual, get that one)
  JavaNNS 1.1
  Mac OS X 10.6.8 (10K549) / Darwin Kernel Version 10.8.0 (i386)