Overloading names in that way is a great way to introduce subtle bugs and make code hard to understand. If it's an array it likely contains more than one item so using a plural form of the name (@wwns) may make sense. Alternatively I'd use the slightly more generic variable name $name for the input variable.

Oh, and don't use our as a substitute for my, especially as a temporary variable - it doesn't do what you think it does and is not at all appropriate. I'd tend to rewrite the thing as:

#!/usr/bin/perl
use warnings;
use strict;

while (1) {
    print "Enter the wwn: ";
    chomp (my $name = lc <STDIN>);

    last if $name eq "q";
    print join (':', unpack ("(a2)*", $name)), "\n";
}
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Update: s/own/our/

I quite agree with GrandFather.

In fact, I think I would go a bit further and advise the use of more 'documentary' scalar variable names:
    chomp (my $raw_wwn = lc <STDIN>);
    ...
    my $fixed_wwn = join ':', unpack '(a2)*', $raw_wwn;
    do_something_with($fixed_wwn);