If you have been banging head about an AO-Java application that run in development but not standalone, then I found a solution which I am sharing.
You need to both compile AND RUN it with a 32 bit version of Java JDK. ie "C:\Program Files (x86)\Java\jdk1.7.0_07/bin/java" -jar "C:\Tools\ParseArcMap\dist\parseArcMap.jar"
If your default java version is a 64 bit, then double-clicking the jar wont work.