I am programming both in Perl and Java a lot, my experience with regular expression usage in Java is that it is always verbose and clunky to set up. Of course the regexes are very similar, as the other monks already commented, but a regex always feels like a stranger in Java-Land.

The speed I am mainly interested in (and where most times the real difference lies) is how fast and natural I can express what I want, and therefore for parsing and matching Perl will always be a lot better. With Perl, I often can write a one liner on the command line, and I am done.

Of course, if you have a big project where regexes play only a minor role, it may feel different, but then the focus lies elsewhere.