I usually just use print statements for debugging. (That's what Larry does; he said as much last week.)

do_this();
print STDERR "Did this!\n";

do_that();
print STDERR "Did that!\n";
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There's room to get more creative, but I'm pretty happy with the code in one window and a tail -f error.log in the other.

My suspicion is that there's a conflict between Apache's built-in Expat and the Expat required by XML::DOM. It bit me once. You'd have to recompile Apache and disable the Expat target to test that, however.