Ideally, the warning should be part of the link. So a link like "terms & conditions" would need to be adjusted to "terms & conditions (this link opens in a new window)".
so it's best viewed in it's own tab
Sez who? Do you not think that your site visitors are quite capable of making that choice themselves using the controls in their own web browsers? As it stands, you're trying to hijack those same browsers and taking the user's choice of how to view links etc away from him/her. That's a bit like me standing behind you and knocking your hand of your mouse every time you just wanted to click on a link & insisting you open the link in a new window instead. It's annoying, frustrating and just darn wrong.
Instead of forcing this upon users (some of who will have a very good reason to steer away from any new windows), why not just warn them using something like "terms & conditions (this page is best viewed in a new window)" and then let them chose?
Apart from anything else, the approach you suggest will create insurmountable problems for some disabled users and, as equal web access for disabled people is often mandated by law, this could place your site on the wrong side of said law.