The Paterek manual at
http://www.timpaterek.com/tpmanual.htm is an interesting read. I am not an engineer but have worked in the R&D field at IBM and have some natural sciences and math background. It read ok to me but there was no way to do "what if" analysis.
As a lay person my interest comes from being in the middle of specifying a custom frame build. The builder is very knowledgeable but I find myself at a disadvantage in helping guide him other than what "feels" ok in my current bikes and what doesn't. I wish I knew more about the framebuilders' art since it is over 100 years old. There would seem to have evolved a bunch of well known "solutions" and "rules of thumb". Something in between Sheldon Brown's guide
http://www.sheldonbrown.com/frame-sizing.html and a finite element analysis software package.