Being lazy I would suggest using Regexp::Common::balanced.

Taking into account all the problems with writing a regexp for balanced delimiters I wonder how it can work in the generall case, but I hope it works.

Update: It's not really equivalent to the other proposed solutions. But it has a clear semantics that shoul be applicable in many cases.

Here is an example:

use Regexp::Common qw /balanced/;

$r = qr/$RE{balanced}{-begin => "<%"}{-end => "%>"}/;

@list = ("aa<% <% %>bb", "aa<% %> <% %>bb", "aa<% <% %> %>bb", "aa<% >
+% %>bb");

for (@list){
    /($r)/;
    print "$` \t| $1 \t| $'\n";
}
[download]

and the output:

aa<%      | <% %>     | bb

aa     | <% %>     |  <% %>bb

aa     | <% <% %> %>     | bb

aa     | <% >% %>     | bb
[download]