There's no easy way to do this save for parsing the replace-with string yourself. There's a rename script which comes with Perl, that allows you to pass Perl code as the first parameter, which it then executes for every file, passing the filename in $_ and moving the file if the code modified $_.

Note that $1 et al are most likely subject to parsing by the shell on Unixoid systems, as are parens and the backslash, so if you want to use them, you'll need to enclose the parameters in single quotes to prevent those characters from being interpreted by the shell.

Probably the sanest solution would be to use a printfish syntax for the right side, composing a new string from the captured bits for every match. Something like this (untested; esp. the pattern).

my ($re, $fmt) = @ARGV;

function reformat {
    local $_ = $fmt;
    s/%(?:(\d+)|.)/$_[$1] if defined $1/ge;
    return $_;
}

# ...

$re = qr/$re/; # precompile

for(@list_of_files) {
    next unless (my @capture = /$re/);
    rename $_, reformat(@capture);
}
[download]

Makeshifts last the longest.