How do I uninstall Java?
After some reading:

JVM in /System is system-wide installation of Java, which is always installed on Snow Leopard, and is updated through standard Software Update mechanism.  I don't think it would be good idea to remove this JVM, but haven't tried it ... maybe nothing bad will happen (if you don't use Java).

My JVMs in /Library are from Java Developer Package, which also contain sources and documentation. It seems that it is OK to simply remove them. After I have removed them, java_tool is no longer showing them.

(After this, I've updated my Java to latest one available from Apple, and also installed latest Java Developer Package, which added new JVM into /Library again. Since I use Java sources and documentation in my IDE, I will let it live).