CPU Clock Speed (GHz);
Amount of RAM (GB);
Amount of Video RAM if relevant (GB)
Are the most important. You can Also look at:
HDD Size (GB/TB);
HDD Speed (RPM or Flash)
CPU Number of Cores
Those are the best ones I can think of right now. The most common point of comparison is CPU speed. You should look at all of these numbers individually, decide what's important to you, and make a decision that way. Do you need to watch and store videos? Then HDD size and the video card are the most important, and you can sacrifice CPU speed. If you're playing video games, then CPU speed and video RAM and standard RAM are important. Certain processes rely more on the CPU.
But the Windows Experience Index is not a good way to compare computers. It is not even a good composite score, as it just tracks the lowest subscore.
Basically, overall performance scales with CPU clock speed, and for the most part, if buying retail, you pay more for better equipment. There are a few exceptions, and that is why it is good to look at all of these numbers, but for the most part this holds true.