Bike fit is, like economics, a dismal science. The idea of a simple calculator, though it can point one in a general direction, can also steer one astray ... though many, many cyclists would like things to be so easy.
I like to think fitting a bike more akin to tailoring. You don't go to a fine tailor and expect to have them punch numbers into a calculator; you expect to have your parts (not bike parts) measured, a thorough enquiry about your personal needs, physical limitations/quirks and only then will the fitting process begin.
A spanner in the works of many bike fits is the fact that the person looking for cycling comfort already owns a bike that is, if not in whole, then in its components, unsuitable for the kind of riding they actually do. For example, they are a recreational rider, but they've been sold on a bike/position suited to racing.
That's the extreme case. Often, a bike can be tweaked by swapping out a stem, adjusting saddle position/height, and/or repositioning feet on pedals. All these factors, however, go into the final "fit" and if one thing is grossly off (say, the top-tube is way too long), no amount of tinkering will make it work.
There are a lot of canards that have spread through the bike fit "industry" that simply don't work for everyone as some kind of one-size-fits-all gospel. In the end, the rider must listen to their own physical feedback and adjust accordingly. Also, one person's bike fit is not cast in stone--or steel, or carbon fibre--forever; it's an evolving relationship, even by season.
I have a bike fit page at VeloWeb that advances this philosophy, with some tips that give a starting point for cycling comfort. A fitter that does not follow the usual "program" can be a real help, but beware of those who would squeeze you into an ill-fitting suit.
