ProGuard is a free Java class file shrinker, optimizer, obfuscator, and preverifier.
I'd seen a few mentions of ProGuard and then when I was updating to the latest version of the Guava library I saw that they were recommending it. So I decided to try using it on jSuneido.
It shrunk the size of the jSuneido jar from 2.5 mb to 1.4 mb. That's pretty good for an hour or two of setup.
I haven't tried the optimization yet, partly because the Guava instructions disabled it. I'm not sure why.
ProGuard also does preverification which should improve startup time, although that's not a big issue for the server usage that jSuneido is aimed at.
It took some trial and error to get a configuration file that worked. I'm not sure it's optimal yet. I still get some warnings from Guava (mentioned in their instructions) and from jUnit, but they don't appear to cause any problems.