Have your tried the "alliance" websites themselves? Which airline mileage program are you a part of?
I'm a member of a couple of mileage programs, but the only one I care about is the Alaska mileage because that's the only one where I ever get the chance to use the miles before they expire. Alaska's not a part of any of those alliance web sites, though they do codeshare with some of the airlines which are members of some of those alliances.
The ideal layout that I'm looking for would be to have the same system as existing travel web sites, but then have their search results allow me another column of data for sorting how many miles I'd earn on my selected (or perhaps more than one selected) codeshare. Like I could have one column sorting "this flight would earn me x alaska miles" and another column for "this flight would earn me x USAirways miles", etc. Perhaps with additional data for how many EQM miles, as Dan suggested.