One thing I do miss about Java is the threading model... if Perl's threads were better, it would make some of my programming tasks easier. (fork
and shared memory don't really cut it, and named pipes or local sockets aren't as nice).
Another thing easier about Java is that most people have some sort of JVM installed, at least in their web browsers. Yes, there are a lot of differences between the three major variants, but if someone has a modern version of Windows installed, they have Java.
GUI programming... it's a wash, either way. Perl's nicer in some ways, depending on your widget set, while Java has more widgets built in.
I'm a whole lot more productive in Perl, though, and I'm a better programmer for learning it. If you have the time to learn both, you'll benefit.