Pipes are special in regexpen, therefore you need to escape them, for example using the \Q trick:

use strict;
my $string="altcategory=||";
$string =~ /(.*)\Q||\E$/;
print $1;
[download]

or by introducing leaning toothpick (or cross-eyed plumbing in the case of pipes) syndrome:

$string=~/(.*)\|\|$/;
[download]

CU
Robartes-