The editors of the journal Neuron are now publishing readers' comments on the journal's website. Comments can be made online for any paper published in the journal, including all of those in the online back archive.
Neuron is owned by Elsevier, and the decision to publish online readers' comments is an interesting one. This is because although Elsevier is one of several publishing giants who have been vehemently opposed to the open access movement, it is now following in the footsteps of the open access Public Library of Science journals, which began publishing readers' comments earlier this year. At PLoS, readers' comments are moderated by Bora Zivkovic.
Here are the guidelines for publishing comments on Neuron.