This is a very simple and yet common task in my architectural modeling, but I’ve not yet found a fast way to do this. My current method is not very efficient.
I vote for finalbarrage’s alternative, if not too late in modeling.
Note: Mano-Wii addon is included in buildbot’s Blender builds, as it turns out. Tends to leave not needed verts around but is really cool nevertheless.
There is one more addon which could be interesting for such cuts - http://blenderlounge.fr/forum/viewtopic.php?f=26&t=1534