Fer instance: on my Eisentraut, which was built for full-length brake cables, the top tube (rear brake) cable guides aren't in a straight line like they are on most bikes. They follow the natural curve of the brake cable, which makes for (ever so slightly) smoother rear brake action. Also, Albert's pretty well known for almost never using stock tube sets, even on his stock bikes, like mine. From what I know, it's a mix of Columbus and Ishiwata, each tube hand-picked for its purpose. And on the subject of tubing, very few tubes are perfectly straight. Mitering the tubing so that the "bow" in each tube is in the centerline of the frame makes for better alignment. And where should the long butt in a tube go? At the bottom bracket, to make it stiffer? Or at the head tube to stiffen up the steering? These are all considerations that an expert builder will take into account when optimizing a frame for the intended rider and usage. Admittedly, these are all subtle differences, but when they're added up, it can make a noticeable difference. And I'm sure I've barely scratched the surface...

SP
Bend, OR