Trackback authentication
Jacques Distler: The anonymous nature of the internet makes the problem of “identity” a hard one. In physics, when we encounter an intractably-hard problem, our most frequent dodge is to redefine the problem to one which admits a solution, and hope that the result is a “good-enough” stand-in for the original problem. In that spirit, I (re)defined the problem as reliably associating comments posted with the websites of the commenters.
Just a suggestion: a lesser, but very much related and much more tractable, problem is trackbacks. The reason why it is more tractable is that the trackbacks are issued by software which could reasonably be expected to have direct access to your weblog's private keys. This could make signing totally automatic - simply check a box once, and your template could be updated and all future trackbacks would be automatically signed.
The signatures could be passed as a new CGI parameter or as a HTTP header. Neither would likely affect any existing software that wasn't expecting this information.
Once trackback signing is widely enough adopted, people may feel comfortable turning off the ability to accept unsigned trackbacks. And then much of the infrastructure will be in place to tackle the harder, and more important problem, of comment signing.
The key nut to crack there is to make it easy and painless to sign a comment.