Threaded or Flat
If you noticed in the other threads that have various replies, that they are threaded. By which I mean the replies are kept together. See Forum Test for an example of what I mean.
Optionally it "flat" comment thread I believe will follow the format of our forum of our 2.0 site. Each new reply is added to the bottom and not grouped with the message it is replying to in the thread. At least to my understanding I believe that is how flat will work.
Without being able to automatically insert a quotation into the reply from the message we are replying to, I think threaded may work better. But perhaps it may be harder to follow. I guess we will see how it pans out in use here.