Yeah, even if it seems like a good deal, you're still paying for a bunch of crap you don't need. Most prebuilt computers that come from companies such as Dell also stick in their useless software into the OS installation and really hog and slow down your computers performance.
Building yourself means you know EXACTLY what hardware and software is gonna be going into your machine, with a Dell, you generally don't.
Most of the other posters have pretty well summed up the other flaws that you'll get when buying a Dell.
Intel C2D E6320 / AMD Athlon X2 3800+
Gigabyte 965P DS3 / DFI nF4 Ultra-D
2GB OCZ Gold PC2-6400 / 2GB OCZ Gold PC4000
eVGA 8800GTS 320MB / eVGA 6800GS 256MB
150GB Raptor / 74GB Raptor
2x500GB / 320GB
OCZ GameXStreme 850w / OCZ StealthXStream 600w