I did a quick and dirty forum a couple years back that now serves up hundreds of new threads a day (having tens, sometimes hundreds of messages each).

My solution was to store a comment thread in display order in the database with hinting as to how deep in the heirarchy the comment is. Optimizes for output, although with some cost every time something gets posted. Luckily, for most forums, views outnumber posts by hundreds of times.

The one issue that system has is that if you're doing a lot of reordering, let's say from quality scores. In that case you'll basically have to remake the thread after every post and after vote that makes a difference. Not recommended...