Markup should only ever be concerned with document structure, not behaviour, which is why there's no way to create a popup with a strict doctype.
If you want to manipulate behaviour, make use of javascript - preferably unobtrusively (Don't use inline javascript, assign all event handling through an external script, allow the 'event' to work if the user doesn't have javascript enabled).
Depends on the method behind the popup and the design of the blocker.
User initiated popups [clicking on a link] will, and should, be allowed through, while popups automatically spawned by a script should be blocked as they're the genuine annoyance.
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