One thing I notice sometimes is that insightful, well-written comments will sink to the bottom of a thread (presumably from posters without a high karma), leaving less interesting comments percolating at the top of the discussion (presumably from posters with high karma). That's a shame and I don't really know how it could be resolved. But it's also a problem on many discussion sites (Reddit, Slashdot etc)

In long threads, I suspect many posters will never scroll towards the bottom of the discussion. Thus, the comments at the top of the discussion continue to accumulate upvotes while good quality comments further down never get a chance to rise up. But I guess that is more due to user behaviour rather than some algorithmic logic.