Edward Felten writes about reputation in filesharing networks:
A file-sharer, though, doesn't want to upload too many files, because each upload uses up part of his network resources. A file-sharer suffers if his reputation gets too good, so a reputation system may create a perverse incentive to behave poorly sometimes. Indeed, a group of friends might conspire to trash their own reputations, so as to ensure themselves unimpeded access to each others' files.
That would be true if the reputation were tied to raw service numbers, but if your reputation were tallied as your good-to-bad upload ratio, that wouldn't be so bad. And of course you'd still have the rate limiter controls you do now: if you're so reliable that everyone and eir cousin want to download from you, just make sure you set a maximum throughput/uploads count with which you're OK. People might queue just to get files from you, but as long as your reputation doesn't include those people who want to download but can't, you won't get hammered for requests.
As for who tracks the reputation, can't PGP-style web of trust do that? Sign someone's key when you get a good file from them to enhance their reputation. (That's a little funny, actually, because that means that, unlike the eBay model, you can't vote against someone. If you could, the person you signed against can merely not give your anticert when someone asks for eir key. And I guess you'd have to check every signer for repudiations... Maybe you could give your anticerts when people ask for your key. If you're well-trusted, it'd get around.)
