I have always been a confirmed vertex modeler [having come over from Strata], I have been a 'point-puller' from Day One. One of the frustrations about the Vertex Window is that if Object A is in front of Object B, or partially obscurred, or inside, it's next to impossible to select it, much less just a few of it's vertices, without selecting and dragging facets of the other object. The other day I had the vertex object displayed in Wireframe, and lo!, I could access the points that I wanted. Just don't click directly on any unwanted points or polygon lines, and you won't disturb Object B. You may get a few extra points selected as you marquee, but hold the Shift Key and click on them until they go away. Then go back to Shaded View and keep working. The image shown is of a doorway molding around the entrance of a locomotive.

I usually keep my ortho view in shaded mode and the top left and front views in wireframe for exactly this reason. It's very handy. Hadn't really thougt about switching the views in the windows all the time -- that might be a better workflow tool.... Will have to give it a try! - Dex

I've hit that a few times as well. I then start naming selections and hiding stuff. Although this isn't ideal when you are trying to position with respect to the stuff your are hiding. :/ In that case, temporarily move the points into clear space and then back. Still not all that simple at times.