Apparently, there's not much difference. GTK# programs (Tomboy, BLAM!, monodevelop) generally rock, so if Java's equal to C# why aren't we seeing lots of kewl apps in Java, and is Java ready for the desktop (at last)?
I used to want to write lots of stuff in Java (but never did much) because the machines (Sun ELCs, SGI Indys) were too slow, Java 0.9/1.0/1.1 were too unreliable and the graphics toolkits sucked back then.
I've recently registered Systemo as a place to learn-and-release C# and GTK# programs. Perhaps Java and Java-GNOME programs might slip in there, too.