$re = '/\[\[((?:(?!\[\[)[^()])*)\s+\(((?:(?!\[\[)[^()])*)\)\|(.*?)]]/m';
$str = '[[<name> (<identifier>)|<name>]]
>>>
{{<template>|<link>|<identifier>}}
====[[<link #1>]] [[<link #2 name> (<link #2 identifier>)|<link #2 name>]]====
[[<link #3 name> (<link #3 identifier>)|<link #3 name>]]';
$subst = "{{<template>|$1|$2}}";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php