What I have used in the past, which would be great to have with live prices, is a spreadsheet with a categorised shortlist of CPU, MB, RAM, Case etc. down the left-hand side, and a set of columns with quantity fields to select which parts would go in the build, so you can pluck parts from the shortlist to include in the build by putting a "1" in the Quantity column, and compare the total price of different builds, like this:
How about being able to compare lists? Perhaps you could line up a couple of lists in columns and compare the components from each category inside them?
The "Config 1" and "Config 2" sets of columns on this spreadsheet are the two build options, and I can compare the total price at the bottom (ignore the tax calculations, they are for the old GST and tax rates).