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my %TAG = (
   ftp     => 'ftp://',
...
   pad     => '/index.pl?node_id=108949&user=',
   DEFAULT => '/index.pl?node=',
);

# takes care of [tag://target|alt]
$chunk =~ s/\[(\w+):\/\/(.*?)\|([^\]]+)\]/<a href="$TAG{$1}$2">$3<\/a>
+/g;
...

# takes care of [target]
$chunk =~ s/\[([^\]]+)\]/<a href="$TAG{DEFAULT}$1">$1<\/a>/g;