Apologies for resurrecting this old thread again but some peeps may not have seen it first time around and, since the last post over a year ago now, there have been a few new finds of stones under churches which may be of interest. For example the stone under the pew at Alphamstone that ocifant and others have already mentioned now seems to have a twin. I don't know if it's only recently seen the light of day but the stone lies opposite the one that's under the pew. This second stone is embedded in the north side of the west wall - http://www.themodernantiquarian.com/img_fullsize/70874.jpg What's interesting is that both the sarsen under the pew and the one on the north side of the west wall seem to be placed either side of the old west entrance (now blocked) to the church.
See also - http://www.northstoke.blogspot.com/ Tuesday, 7 October 2008 for up-to-date observations on Alphamstone.