For one thing, you can cut out a number of arrays by combining what you're doing. From a quick glance, you don't seem to be using @xfilenames (and the like) except as a temporary data structure. Instead, do something like:

my @filenames;
my @titles;
my @headings;
my @stuff;
foreach (@pages) {
    chomp;
    if (/^\*{4}filename.ext\*{4}/) {
        s/^\*{4}filename.ext\*{4}//;
        push @filenames, $_;
    } elsif (m/^\*{4}title\*{4}/) {
        s/^\*{4}title\*{4}//;
        push @titles, $_;
    } elsif (m/^\*{4}heading\*{4}/) {
        s/^\*{4}heading\*{4}//;
        push @headings, $_;
    } else {    
        s/\*{4}stuff\*{4}(.*?)\*{4}endstuff\*{4}/sg;
        push @xstuff, $_;
    }
}
[download]

You now have 4 less lists, thus cutting your memory usage for data structures almost in half.

Note - don't declare all your variables up-front. That's a very C-like thing to do. Declare them when you need them, as you need them. Declaring a list or hash takes up considerable memory, as Perl will pre-declare like 50 (or so) elements that just sit there.

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