Well, you seem to have the conversion down good (unless I really don't know what I'm doing), but I think you've got far too much code. :) A lot of your testing (as mirod says) could be simplified. Here's what I came up with:

use strict;

sub bin2dec {
   my $arg = shift;
   return unpack("N", pack("B32", substr("0" x 32 . $arg, -32 )));
}

my ($binary, $decimal);

print "Please enter a binary number: ";
do { chomp ($binary = <STDIN>) } until (length $binary);
die "That's not a binary number, dude...\n" if ($binary =~ /[^01]/);
$decimal = bin2dec $binary;
print "$binary = $decimal\n";
[download]

My test is similar to mirod's, but it works by checking to see if there's anything besides 1 and 0, instead of if everything is 1 or 0. I also have the program wait until something is actually entered on the line... but these things are subject to personal taste, IMO.

You'll notice, though, that my bin2dec sub doesn't use any global variables... you'll want to stay away from doing that except in certain situations, as it makes your code less adaptable later on.

That all being said, though, it's not bad code, it's just difficult to understand with the myriad of unnecessary tests in there. I hope that helps... if you've got any more questions, get an account and /msg me! :)

His Royal Cheeziness