The review system for research projects in Italy (during the last few years; it is possibly going to change now) was based on comparing the opinions of two different anonymous referees. At some point the two referees have to exchange opinions with each other and reach an agreement, while remaining anonymous. In practice, this is achieved by channeling communications through a website based at a central location. I post my comments, the other referee can read them and post his comments, etc. Since we both know that our exchange is watched by some official at the Ministry, we feel some pressure as to not revealing our identity. I think this works pretty well, and should work also for peer review.
Actually, several journals have already an electronic system for reports; at the moment it is a little awkward to use it as a communication tool, because of the many steps involved (the messages must be approved through the chain referee->editor->chief editor->editor->author or something like that), but it should be quite easy to make it faster and transform it into a supervised direct channel between referee and author.