Here are just a few other ways you can fine-tune a "link recommendation" algorithm beyond just the standard "show highly rated links at the top" technique:
1) Devote a portion of prime real estate (e.g. homepage) to new or trending links, as Reddit does.
2) Give higher placement to submissions that come from someone whose previous submissions the user has upvoted.
3) Give higher placement to submissions that come from the same source as previous submissions the user has upvoted.
4) Give higher placement to submissions on which a person has commented whom the user has previously upvoted.
One way I think HN, Reddit, and other link-recommendation sites can put power into their users' hands is to allow each user to tweak the recommendations algorithm to suite their own preferences.
For instance, one user might want half their homepage to be filled with trending stories, rather than popular stories. Another user might find Technique 2 above to be useful but might not want to enable Technique 4.