I believe it should be possible to score user reputation using an algorithm similar to page rank.
The idea is up-voting from a higher ranked stack user should weigh greater than an up-vote from a lower ranked user. A more important user is one who has received up votes from important people (just like google's page rank, a page is important if it is linked to by important pages)
This will solve problems of the kind where people create a clique and keep up-voting each other within the clique (I don't know if this happens, just possible). It feels like a more equitable system than the current static scoring mechanism. It would also give opportunity for bright and young minds to move up the ranks on stack faster.