I do a lot of trans-faction transfers through the neutral AH (the autobuy feature is a life saver, never had anything sniped) but it messes up the avg value of item seriously due to the amount of 1c transactions. There should be a separate category for the neutral AH, or an option to register it as such (I know it uses values from the other factions to facilitate making neutral deals, but still).

I guess you pick up a transaction's faction based on the character, but I think you could discriminate neutral AH based on location.