During my recent visit to the Googleplex, I sat down and interviewed Matt Cutts. One of the things I wanted to get a handle on was how Google handles links encoded in Javascript, or that go through redirects.
A lot of time people implement click throughs so they can analyze the outbound link traffic. Matt told me that there is a recent proposal someone made to add a ping attribute to links, which would allow for that type of tracking without having to send the link through a redirect. Interesting idea.
More importantly, the bottom line is that Google does try to track these links, and still pass PageRank appropriately. This is good news for SEOs who groan when they get a great link from a .gov or .edu site that goes through a redirect. Google will still try to pass PageRank for that link. However, as always, the best practice is to try and get the link as a direct link.