This is a good reason to use a /ex block to perform the magic.

local $/;
my $data = <DATA>;
$data =~ 
    s{\[([^\[]*)\]}
    { 
        my @bits = split '\|', $1;
        @bits= map{ s/^\s+|\s+$//g; $_}grep{ ! m/^\s*$/ } @bits;
        if ( @bits == 0 ) {
            # error handling just return original
            qq![$1]!;
        }
        else {
            # may want to auto add
            $bits[0] = "http://$bits[0]" 
                unless $bits[0] =~ m/^(?:https?|ftp)/ 
                    or $bits[0] =~ m/[a-z][A-Z]|[A-Z][a-z]/;  #camelCa
+se
            if ( @bits == 1 ) {
                qq!<a href="$bits[0]">$bits[0]</a>!;
            }
            elsif ( @bits == 2 ) {
                qq!<a href="$bits[0]">$bits[1]</a>!;
            }
            elsif ( @bits == 3 ) {
                qq!<a href="$bits[0]" target="$bits[2]">$bits[1]</a>!;
            }
        }

    }gex;

print $data;

__DATA__
This is an error []
This is OK [www.perlmonks.org]
This is OK [www1.test.com|test page1]
This is OK [www2.test.com|test page2|new]
This is errorish [www2.test.com|test page2|]
This is errorish [   www2.test.com    |    test page2     |    ]
This is camelCase [   camelCase|Local Link in Blog | new ]
[download]

This allows you to handle errors gracefully (ie tolerate whitespace errors) and say add http:// to apparently external links and ignore for camelCase links (assuming this is for a blog) ie:

This is an error []
This is OK <a href="http://www.perlmonks.org">http://www.perlmonks.org
+</a>
This is OK <a href="http://www1.test.com">test page1</a>
This is OK <a href="http://www2.test.com" target="new">test page2</a>
This is errorish <a href="http://www2.test.com">test page2</a>
This is errorish <a href="http://www2.test.com">test page2</a>
This is camelCase <a href="camelCase" target="new">Local Link in Blog<
+/a>
[download]