I think you can continue to bank on developing your Perl skills, while Java skills will not necessarily get you a job right away considering the labor market and the overvaluation of Java skills for many projects. But this depends on where in the world you are.

To me this is particularly true if you are studying Perl, Linux, GNU, and Open Source tools together. You learn how things work and are not afraid of C/C++ tools. You have a low barrier to Python if necessary, and you laugh at ASP. So far I have seen a number of projects which have spent tons of money on Java programmer teams and Java application servers, then the money left over is only enough to do something in JSP that could have been done just as easily with Perl. Perl is not the answer to every single problem but it is so extensible, it seems to be applicable to more than any other.

Also I find Perl gives you a laboratory for learning about computing, and it gives you weapons of knowledge which help you be intelligently critical of new systems, whereas intentionally drinking at the trough of watered down corporatespeak you may end up on the receiving end of a lot of b.s. A number of companies still rely on the b.s. rather than listening to their programmers, whether they are writing Java, Perl or something else. I think those companies are going the way of the Dodo.

If your goal in life is to be working on enterprise software in a large organization, you probably want Java. Otherwise, I'd try to take in a swath of things, and learn Perl and go everywhere it takes you. Learn a little Java too so you know what is going on.. though it will take longer to become able to do something useful with it than it may with Perl. You can master programming in either language but I'd say what you want to work on is polishing your systems skills regardless of the language in which you operate. If you understand the foundations of programming and computing you can switch into other programming systems (which frequently appear) without losing your investment.