depends on the deal
Some custom PCs can be allot cheaper, and you get exactly what you want and non of what you don't.
But u never know until you start comparing. Sometimes HP, Dell, Acer, ect. come out w/ insanely good deals on decent machines
I personally always build my tower/desktop systems so I can maximise its capabilities and get some serious tuning going on, far more than any branded system can do - even the boutique vendors like Alienware, Voodoo, etc. Plus they always come out cheaper spec-for-spec or higher spec price-for-price.
For laptops though I can't be bothered building my own so I always look for packages and offers.
It really does depend on what you want in a system, because for the entry-level and basic stuff that you'll never really upgrade you can usually get some really good deals from the Dells and Acers of the world, and at the bottom end of the price scale I've never been able to match, let alone beat, a Dell price-wise.