As for Perl vs Java, judging from recent conversations on boston.pm, PHP is seen as a far more direct threat.
I agree. I code in both. I like both. However for what I do (web/database intergration) PHP is my 1st choice. Perl was the defact language for CGI and dynamic websites. Now PHP (and to some extent ASP) has replaced it. Perl has it's place for a lot of background tasks and for anything too complex for shell scripting.
Java doesn't really compete with Perl (or PHP) in any of these places. I don't understand what all this Java vs. Perl stuff is about.