The N&R's new real-name-only commenting policy has gotten a fair amount of reader response, with several people saying the change will keep them from contributing to future threads.
Gauger's right that there's no free speech issue involved, but the readers who say they fear speaking out on social issues under their own names are pretty convincing. The argument for moderators, including volunteers, seems like a good one.
I was more in favor of the new rules when I started the thread than when I finished it, but it's not a problem with an easy answer, or one that need have a uniform solution for every site.
FWIW, I haven't found pseudonymous commenters here to be much more or less obnoxious than real-name commenters, although the most extreme (racist, misogynist, etc.) commenters have been anonymous.