Is there any reason the following shouldn't work?
perl -pe 's/\n\n/foo/;'
What you may want to do is this:
perl -pe 'BEGIN {$/=undef} s/\n\n/foo/'
I tried that, but this does not allow me to use "^" to denote the beginning of a line, which is critical to some of the search/replace things I'm doing.
Any other thoughts?