Much effort has gone on in the various congregations I've belonged to and visited in distinguishing the building in which the Church meets and the Church itself. Much discussion has been made of the fact that we are many denominations but one Church.
In light of those ideas, phrases like "our church" and "that church" have long bothered me. Even the names of our congregations - Rhea's Mill Baptist Church, 1st Pentecostal Church, Oak Avenue Christian Church - nag at me. For me, these are our congregations of THE Church. Therefore I've used the term congregation in place of church when referring to a local body of believers. Granted, it is more cubersome and more letters to type, but I think it conveys the idea that we are just parts of the whole and that we acknowledge that the fellowship that meets a half a mile away from ours or the one whose worship time is more lively are each filled with our siblings.
I'm not suggesting some type of ecumenical idea. To the contrary, I think it says that it's fine for us to have differing styles, sizes and non-essential beliefs.
On the other hand, I'll not be using it do describe Mormons, Jehovah's Witnesses, Scientologists or any other cult even though there may be members of the Church attending in those places who have yet to realize that they're in the wrong place.