Generally, discussion boards for techies opt for full threading, while nontechie boards are completely flat. Both methods have significant flaws that annoy me to no end.
Stackoverflow has a format that I hadn't seen so far: A flat list of answers (sortable by score or date), with a flat, chronological list of comments per answer (hidden by default).
I love it! I think that it might be a superior choice for almost any forum.
Has anyone seen it before? Does it have drawbacks?