Seems like everyone and their mother has an opinion on the “right” way to have comment threads. Currently Subtext supports the same model as .TEXT did, a simple linear sequential list of comments. It is simple and gets the job done.
The 37Signals blog addresses the question of comments and presents several examples of how different sites handle it.
Personally I like the first example. It retains the simplicity and fluidity of the linear approach, while adding a bit of useful meta-data. What do you think?