The average punter cannot embed a link in an actual YouTube video so that it points to an external site. They can add a link to the video's description or use YouTube's Annotations to add certain types of actions - but not offsite links.
The LinkedTube site lets you take a YouTube video and place your own overlay on it. That's a start but it means the link layer doesn't appear on embeds elsewhere. The video affiliate platform Coull lets you build a similar video, with their overlay, for shared affiliate links. I'm going to come back to affiliate marketing in just a second.
However, it is possible for brands with certain spends to create YouTube videos with external link overlays. For example, check out this brand new video from Bethesda Softworks that shows off the (gory) pre-order bonuses for gamers who buy via Amazon (different shops have different pre-order bonuses).
I watched this video with an affiliate's hat on. I wanted to blog about the pre-orders and link to the sites taking part. The catch? The video links are affiliate marketing no-go zones. I can't get my tracking links into place on them. Rather than being a strong affiliate marketing asset, these videos are something of an leak.
That said; unless you watch the video on full screen mode it is quite hard to click on the link! YouTube's progress bar pops up to block your mouse.
The advantages of embedding links into these videos are clear - traffic.
In this particular example, a number of different retailers are involved and Bethesda might actually benefit from their attempts to promote their version of the video (helping it match [Dishonored pre-order] and related searches on YouTube).
I suspect the affiliate leak risk wasn't considered - wrong teams - but I also suspect only a few fan site affiliates will shy away from running the videos because of the leaky link. That'll be good news to everyone involved. It'll only be the hardcore affiliate model retailers that now consider the vids off limit.
The oppertunity for Google to do something very impressive with the Google Affiliate Network and YouTube is clearly there.
However, as we're yet even to see Google Affiliate Network action for Google Play my suspicion is that we're in no danger of Google integrating affiliate marketing into a far more liberial external link overlay policy any time in the near future.