Multiple HTTP GET parameters with the same identifier

If you can change the field name to include [], then PHP will create an array containing all of the matching values:

http://www.example.com/index.php?id[]=123&version[]=3&id[]=234&version[]=4

If you don't have the ability to change the field names, then as you say, you'll have to parse the querystring yourself.

According to this comment from the PHP manual, PHP's query string parser will drop duplicate params... so I don't think that PHP is a good fit for what you want to do (except in that it has the same capacity as javascript to get the raw query string, with which you can do whatever you want)

Assuming you have some control over the request, suffix the name with [] and PHP will generate arrays instead of dropping all but one.

http://www.example.com/index.php?id[]=123&version[]=3&id[]=234&version[]=4

Since they are pairs you'll probably want to fix the order they appear in using indexes.

http://www.example.com/index.php?id[0]=123&version[0]=3&id[1]=234&version[1]=4