with the caveats as described above (++), you could pull, and sort the parameters. You're then left with a simple string comparison.

use URI;

my $u1 = URI->new('http://host/bob?jack=2&joe=1');
my $u2 = URI->new('http://host/bob?joe=1&jack=2');

if ( sort_query($u1->query()) ne sort_query($u2->query())) {
    print "They're different all right\n";
}

sub sort_query { join('&', sort split /&/, $_[0]) }
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UPDATE: Ack, updated after ikegami's comments.