For domestic U.S. trips this should not be such a huge hassle anymore now that TSA is/will be requiring boarding passes prior to getting to the gate. Just go to the gate agent and tell them you want to change the frequent flyer number for that segment, chat them up, ask the how their day is going, talk to a real human being, thank them for the trouble, and board your flight...

As to alanw's remarks that this is somehow cheating the "system" shows supreme ignorance of the current state of the frequent flyer system as designed by the airlines.