For example, links received in email, if you view the email via a webmail client gmail for instance, and click on the link, it will open in a new window.
I think it depends on the % of users that will want to go back to your app after looking at the link. And with ajax type apps, the back button just doesn't cut it.
The "Strict" standard, rightly, enforces a division between content (XHTML), design (CSS) and behaviour ({Java|ECMA}script).
If you want links to open in external windows, attach a behaviour to the link class with JS. Just make sure that behaviour is off by default, though, because otherwise people like me who know what we're doing won't use your site.
It's not obnoxious if you consider that some people really don't understand how the web works or what the difference is between sites. In that case it's a convenience.
This is an idea which should be left as a "best practice," but allow for reasonable differences.