At PubCon Austin I had the chance to discuss this with Matt Cutts - specifically in the context of googlebot crawling urls found through form submission. In such situations, Google adds a "virtual link" to the web graph - and it is then active in various kinds of link juice calculation.

I am extrapolating here from form input links to javascript links -- but it makes perfect sense that Google would do the same thing with javascript links that they've learned to parse. In fact, Google has been doing a lot with enhanced javascript crawling in recent months, so I am pretty confident that this is what's happening in the cases you describe.

Part of the answer would hinge on WHAT the onClick event points to. If the javascript function proves to be inscrutable to Google's current crawling technology, then no link juice, I'm certain. However, since you say these "links" are showing in your WMT backlink report, it sounds like they could be doing you some good.

The reverse side, therefore, is all the people "hiding" affiliate links in javascript. Is such pointless now or is that another discussion?

What if the onClick and the href don't match up?