Good observations all. We have a pretty good sawyer at Heartwood, and once you find one don't lose 'em. In a whole frame we will rarely have a pine timber that is more than 3/16" out of wind or bowed. That can usually be pulled out during assembly on long timbers. If we find one over that we will use it somewhere it won't matter (such an interior rafter that is bowed) and/or use snap-line instead of edge rule; if twisted we'll split the difference like Mark recommends. We often are leaving the timbers rough, so planing's not an option unless it's on an outside hidden face or top. Scribing and mapping are other options if it's really bad and just a few pieces. Last resort is to get rid of the piece, and maybe the sawyer. One thing to remember is that when square rule was developed aesthetics may not have been as important since mostly barns were timber framed, or houses where the frame would be covered or hidden in the attic.
