I suppose the nice way to do it might be to create a wrapper shell script just called jabref in /usr/local/bin which contains "java -jar JabRef-2.0.1.jar".
You put the jar itself in /usr/local/lib/jabref, and refer to it with a full path. I would also substitute java for the full java path (you can get that with "which java").
So you will probably end up with a shell script like:
/usr/bin/java -jar /usr/local/lib/jabref/JabRef-2.0.1.jar
If the jar processes command line attributes, you might want to pass those through as well.
I would build an install script to create and populate the lib directory, and place the /usr/local/bin script, so that you could then do the same on another machine, and so that you can look there to find and remember where you put the things.