A more general solution (works with any number of filenames in your input string):

use strict;
my $TheLine = 'REFERENCE "z:/bin/JAnalyzer/Justice Analyzer Users Guid
+e.pdf" "package/Justice Analyzer Users Guide.pdf"';

my @Files= $TheLine=~m/"([^"]*?)"/g;
print join "\n", @Files;
[download]

If you want to be really neat you could replace the [^"] by the list of characters valid in filenames.