Go with the custom build. If your unsure how to build you own check out this guide I wrote custom building your own pc
There are a few things you do have to consider though building your own. First is look at the warranty service. Second is troubleshooting and making sure every part is compatible. You need to make sure the ram you want will work with the board your getting. Thats the biggest one right there.
Buying a prebuilt its not so much they charge you more for new parts its the lack of customizing you can acheive and lack of options. Example most places like dell & hp won't let you choose any ram/gpu they give you so many options. If they don't give you a certain option you may have to go to there next series to get that option which is hundreds more.
3rd Part is customizing the new computer. If you buy a prebuilt unless you go ultra high end dell you won't be able to do anything in the bios it will be locked. So that rules out getting a e6600 or q6600 and overclocking it to a higher spec model. Instead you would have to upgrade to say a E6700 or higher to acheive the same performance you could get with a lower end cpu.
Like I said though the biggest thing is if you run into a problem with a custom build your on your own! You don't have manufacture support to simply call dell and say your computer broke. You have to first figure out what the problem is then contact the manufacture of that part and troubleshoot from there.