I've read a lot of people theorizing about how Google counts some NoFollow links. I've never bought into that theory, but I've also not had any strong arguments against it.
Here's a quote from Stephan Spencer interviewing Matt Cutts that is very clear on this issue:
At least for Google, we have taken a very clear stance that those links are not even used for discovery; they are not used for PageRank; they are not used for anchor text in any way. Anybody can go and do various experiments to verify that.