I'm a bit confused. Are you saying you would like internal URLs to open in a new tab?
If so...
In public/js/ipb.js change function openNewWindow to:
openNewWindow: function(e, link, force)
{
var ourHost = document.location.host;
var newHost = link.host;
force = true;
In the same file search openNewWindow again and change the ipb.delegate.register line to:
ipb.delegate.register('.bbc_url', ipb.global.openNewWindow );
This will make it so all URLs that have a bbc_url class assigned to it open as an external link. Should work for all old and new URLs.
If this is an issue with external URLs, then it's a simple setting change.
ACP > System Settings > Forums > Topics, Posts and Polls > Open posted links in a new window