It's a tough one. There are websites that help with such problems, designed to help a person decide between certain computer components. The downside is that a lot of the information can be too technical and can easily confuse.
I know that certain places select different components for different reasons. One being money of course, and that they may be able to get a GFX card cheaper than another store can so they'll incorporate that into their machines.
My advice would be to drop the list of specifications here and links to other places you've looked and maybe one of us can look through the specs.
You're right though, it's a nightmare for most. My OH builds all our desktops and servers. She spends hours looking through specs of each individual components, I just let her get on with it :)