What does the msconfig command allow you to do

A great deal, mostly to do with the startup items and services.
The exact nature varies on the version of windows.
More details here: How to use MSCONFIG: NetSquirrel.com

For one thing you can use it to stop programs that you do not want or need from preloading thus increasing your computer performance. Things like iTunes helper can be stopped you may have to launch iTunes when you plug in your iDevice but it will work fine.