Apple - With Safari, can I allow pop-ups for specific sites?

Yes, with Safari Version 12 or higher, you can allow popups for a specific website. Here are step-by-step instructions:

1. Right click on the URL (when you're NOT in a text entry mode)

   

2. Select "Settings for This Website..."

3. Select "Allow" under "Pop-up Windows"

   

There isn't any exception list for popups in Safari. It's an "all-or-nothing" approach for now.

I recommend telling Apple your thoughts on the Safari feedback page: http://www.apple.com/feedback/safari.html

EDIT 12/20: This answer is correct as of the time it was written. Since then, Apple has added the ability to control popups per site. This answer by @matt-chandler is the correct one for newer versions of Safari. I'm leaving this answer here in case it helps people on older versions of Safari.