There's a link to my site like this: otherdomain.com/jump.php?id=43244 and google counted it as a backlink in the webmaster tools dashboard... I really didn't know they did that!
they have always counted those links, as long as the website does a proper 301 redirect and not a crummy javascript link, or blocks the link another way (meta, rel or robots) then the link is the same as any other link
They've been known to show nofollow as well. I really don't know if what is being showed in Webmaster Tools is a true measure of what counts, let alone how much "juice" is being passed after all the other factors are weighed.
Google is known for their tracking software, so I'm not surprised they follow these links, and probably have for some time. What's new is maybe they're actually using this data now.