I knew this at one time, but my Swiss cheese brain apparently forgot it at some point…

Simply changing <SPWeb>.MasterURL works perfect for WSS and Application pages, etc. However, it's only half of the answer when you toss publishing and layout pages into the mix. In that case, you also need to set <SPWeb>.CustomMasterURL:

site.MasterUrl = myNewMasterURL;

site.CustomMasterUrl = myNewMasterURL;

site.Update();

Dave