Well, on paper those store bought computer can be "better". However, if you're looking to do gaming or something that's more intensive there are a lot of other features and factors of computers that affect the performance than the amount of RAM, type of processor, etc. The speed and latency of RAM that I buy for the ones I build are MUCH better and can really help when gaming. The graphics card is probably the biggest difference to me, and the front speed bus (connection of the processor to the motherboard) can be much better on home built versus store bought computers. That's to just name a few things. One other big difference is that most store bought computer only have a 300 or 350 watt power supply which is just enough to power the stuff that comes in the computer, if you add a graphics card to most any of those computers, you need to upgrade that.
I could go on quite a bit longer, but hopefully this gives you an idea of what the differences are...