Collapsing threads do the job pretty well. And you're always going to get comments that aren't relevant to you, because you're not the only person doing the endorsing. If a comment is useless fluff to you, but gets endorsed by someone else, then you still have a scrolling problem. Not so with collapsable commeents.
They use a very simple system, collapsing posts after a certain depth, and hiding more comments after a certain number (10, I believe) at the level below the top comment (sorted by score obviously).
It works extremely well, and thanks to the fast JS collapsing, it's not at all a hassle to read a subthread that happened to get collapsed if it piques your interest.
It's so simple it may easily be overlooked in its obviousness, but really you don't need a very complex system that is strictly a lot better than no collapsing at all.
What's wrong with (old) slashdot (I mean, technically) ?
While I'm usually a kind of hard core html-first, ajax/js/webapps later kind of guy -- I'd love for the comments to be served up in a json-blob, with a couple of user-settable preferences ("Show only comments rated higher than N, hide threads with lower (median/mean) rating than N, show all direct replies to my comments -- and similar).
I've yet to see any discussion forum solve the problem of long threads with lots of useless fluff floating to the top.