We know "sneaky redirects" are a hot topic with Google. Even the Quality Rater's manual, on page 136, uses a CJ link as an example of a "sneaky redirect". I am now worried about housing my affiliate links in a php script (which I have done for years).
In my niche, I still see at least one website ranking very, very well for a very competitive financial phrase, with nearly 10 affiliate links on their homepage. They are nofollowed, but they aren't housed in a redirect script. This tells me that some affiliate links may be ok, but the method of implementation could cause problems. I did notice Google trying to spider my php script several times back in April/May as if it were analyzing the redirects and their intent. This also showed up in my WMT spider data as extremely large spikes in "time spent downloading a page". Then, I was hit by Penguin 1.0, and possibly even the Panda refresh that came 3 days later.
I want to hear from affiliates who house their links in a script, to see if you were hit by Penguin or Panda (I am not sure if this would be a Panda issue or a Penguin issue -- I could see it as either, because it might be construed as "shallow content" or a webspam technique).
I did notice that one of my affiliate links not only got redirected in my php script, but also did two or three redirects at the affiliate network (which I have eliminated as of about 10 days ago).