Here's a method I like...

In your user settings, set "Note ordering" (in the Miscellaneous section) to "Best" and then use your votes to try to arrange the replies in a thread.

For instance, if there are two replies in a thread and the first (reading from the top) is not as good a reply as the second one, then upvote the second. If that doesn't make it rise to the top position, then downvote the first one. Whether you succeed in swapping their positions doesn't really matter. Recording your opinion of the nodes relative to each other does.

-sauoq
"My two cents aren't worth a dime.";