Threading is a model that allows anys message to have any arbitary number of children.
If you're planning on discussions, threading is evil, as the model discourages sustained interactions.
If you're planning on questions/answers (as you see here), threading is good.
For a linear-discussion board with support for branching and folders containing any arbitary number of discussions, easy customization of look and feel (down to the level of individual discussions), and a proven message-organization model, see:
http://prattle.sourceforge.net/
There are no reported bugs. There are some more changes that I intend to make when I get around to it.