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Can you give an operational definition (or concrete example) of the free rider 'problem'? There are a couple of different things that you might not like about the phenomenon, and I'm not sure exactly which is the problem you're concerned about.
Exclusion is the most common "solution" (auctions and "fair" divisions being specific allocation mechanisms within that). Don't let "free riders" actually ride, and there's no problem.
Exclusion isn't always socially appropriate. If I take a cab home everyday (which I pay for), and a friend can literally take a free ride because her place is on the way, should I "exclude" her if she doesn't want to share the cost? She claims it doesn't cost me extra, I'd be paying for the cab anyway if she lived somewhere else.
But of course I can come up with un-excludable externalities:
I share a house that's in pretty bad shape, and I decide to get some fresh painting done. This is a net benefit to all the housemates, but we would value them differently. I want this slightly more than all the others. So I have to pay the entire amount.