TL;DR: It's fine for video makers who want it, but a separate HTML window with captions and links synchronized with the video would be more useful for Wikipedia.
Popcorn's a great way for video makers and remixers to jazz up their videos, but it's not the best way to bring video elements to Wikipedia articles.
Unless you're just going for a VH1 Pop-up Video[1] effect, a better way to associate video with other material is to synchronize the video with a separate scrolling HTML window, which at a minimum contains the captioning and script of the video. Then instead of overlaying the video with multimedia, you've got an HTML window with all the well-understood conventions for hyperlinks to open a map, open Wikipedia article, cite references, etc. It's accessible, searchable,and translatable. The main reason to show the markers for additional info on the video is when they're spatial, not temporal -- simultaneous links about the church, the subway station, and the undying dream of marketers "Click here to buy Snooki's outfit". That could still be done by adding occasional static imagemaps to the HTML timeline.
Popcorn itself is a player that operates the video and runs the annotations[2] at the appropriate time, which look like popcorn.wikipedia({ "start": 159.28802, "end": 165.22054, "target": "video-container", "lang": "en", "src": "Seasickness", "width": 40, "height": 52.38095238095239, "top": 2.5396825396825395, "left": 60, "transition": "popcorn-fade", "zindex": 1000 });
Google popcorn.wikipedia() and you get their QUnit test[3] :-) , here's their implementation[4]. All the WP popups I've seen don't have a link, so you can't copy the link or open it in a new window. Popcorn requests the entire article from the API[5] but only displays a short extract. Is there a leaner Wikipedia API they should be using?
[1] http://en.wikipedia.org/wiki/Pop-Up_Video [2] http://popcorn.webmadecontent.org/11_ [3] http://popcornjs.org/code/plugins/wikipedia/popcorn.wikipedia.unit.html%5C [4] https://github.com/mozilla/popcorn-js/blob/master/plugins/wikipedia/popcorn.... [5] https://en.wikipedia.org/w/api.php?action=parse&prop=text&redirects&...