I dunno if it's supposed to be secret, but given that Tac posted to his main blog about it, I figure it can't be classified anymore. Check out TestTacitus.org - the new Scoop-driven site that will hopefully replace the creaking old Moveable Type implementation.
I'm a big advocate of threaded discussions, though there is predictable resistance to it from the regulars at TDO v1. I argue in the beta-test thread that threaded discussions make the conversations numerous sub-topics more accessible and will improve and enhance participation. However I should also note that there is also a "nested" mode, which is sort of a best-of-both-worlds approach to flat or threaded threads. Frankly Nested mode is my own default at both TestTacitus and DailyKos.