For config stuff like that, I think DB_File comes in handy... you could easily, from within both programs, do this:

#!/usr/bin/perl

use DB_File;
use CGI 'param';

print "Content-type: text/plain\n\n";

my $filename = '/path/to/database';

tie %hash, "DB_File", $filename, O_RDWR|O_CREAT;
print 'thisvar: ', $hash{'thisvar'}, "\n";

$hash{'thisvar'} = param('webvar'); # modifies from form value

untie %hash;
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Of course, in your non-CGI program, you wouldnt be loading in the CGI module.

Naturally, you could also do something like this:

$filename = '/path/to/config/file';
open(CONF,"<$filename");
while(<CONF>){
  chomp;
  my ($q, $w) = split(/\t/,$_,2);
  $config{$q} = $w;
}
close(CONF);
$config{'variable'} = 'new contents';

open(CONF, ">$filename");
print CONF "$_\t$config{$_}\n" for keys %config;
close(CONF);
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Good luck,
  -Adam