I primarily use square rule, and I only snap lines on timbers that have a pretty good bow to them. Otherwise everything is laid out off the reference face with Big Al. If there is no square reference face then I first swear at the sawyer, then use a framing square to make an imaginary reference edge.
The other Brad: to me, mill rule means no reductions on tenoned members, and typically no (non-structural) housings either. If you don't want to reduce your tenons to a common dimension, you can scribe everything, map them (measure the height/width of every piece, and map them to each joint), or use mill rule, which assumes that every piece that you ordered is exactly as you ordered it. If you're mill ruling a 4x5 girt to a post, then you assume or know that that girt mortise is exactly "5 or 4.75" or whatever.
I like Gabel's point about blurring the lines too.
Tim, is there any evidence of French scribe in your area of Maine? French marriage marks or framing sytles?
Brad