I like Hacker News comment system (though presentation could be better). I like the fact that you see the most relevant comments first. Whereas most other comment systems (even those with points) are chronological.

ps Digg just updated their comment system.

I like threaded comment systems and I prefer digg/reddit since I can collapse them. Really though - how hard could it be? Any capable hacker could write the system to do such a thing in less than a day I would guess.