Kill: remove a link altogether. I already do this via Proxomitron when I'm running Win98.

Lower: anything coming from GeoCities/Tripod/etc. gets a lower default score.

Raise: sites I like get a higher default score.

Trickle-down scoring: sites that high-scoring sites link to receive higher scores. sites that link to low-scoring sites receive lower scores.

Adaptive scoring: links I select receive higher scores. Links I immediately back out of receive lower scores. Links similar to those with high or low scores receive less high or low scores.

Score decaying: adaptive scoring would wear off over time, so a one-week research project on leeks wouldn't throw off your entire system.

Highlighting: I would highlight links based on score on a green-to-red spectrum (the current visited/unvisited system rarely helps me), but this could be very customizable. You could put a little icon next to the link to denote high/low score, for example, or put the actual score in parentheses.

Selectable filter files: people use the web for different things. I'd have different scorefiles for research and entertainment.

The disadvantage of this right now is the bandwidth; you've got to preload linked pages to score them. Other than that, it could be written as a proxy to work with today's browsers.