Sure, go ahead open that can of worms! I'll start it off with what little I know. Just rambling a bit, so it's maybe not too organized.
The Atlas and first Commandos had larger diameter pipes, but that was soon changed to the 1 3/8" diameter used from then on.
I've seen aftermarket and custom Commando pipes in 1 3/8", 1 1/2", 1 5/8", and 1 3/4". They all work ok in the right application. In general, the larger diameter pipes need to be shorter than the smaller ones to work properly in the same application.
The factory race team did some experimentation in diameter and length, and had pipe and megaphone combinations for 750 and 850 engines. They used 1 3/8" and 1 5/8" pipes, and probably tried other sizes, but I don't have data on that. The 1 3/8" pipes gave good mid-range power, but not as good top end as the 1 5/8" pipes. They had pipes and megas for max power, but also some to meet race track sound requirements, that made a little less power. They did use 1 3/4" straight pipes on some of the dirt track racers in the US.
Axtell did a lot of dyno work for Ron Wood's dirt track Nortons, and found the best power with 1 5/8" pipes with carefully sized reverse cone megas. I think Ron may have also run 1 3/4" pipes with the short stroke 750s in the mile races, but I'm not sure about that. It's been a long time, and I've only got an old guys memory now.
For a street bike, it's really hard to find anything much better than the stock pipes with the good peashooters. Of course that's just my humble opinion. Feel free to disagree. But, like for race bikes, it depends on your application. Something like Dunstall's last system, designed by Dr. Blair, would give more mid-range performance, enough that you could tell the difference, but gave up some top end for it. Probably great for most street bikes, but maybe not for the hard core who like to run their street bikes up around 7,000 rpm a lot. The 1 5/8" pipes with Axtell megas that I used on my race bikes gave great race track performance, but the huge flat spot in mid-range would be really annoying on a street bike.
Ken