I totally agree with all of the above posts. Basically, it's more a matter of a preference than cost. Don't get me wrong, I am on a fixed income, so cost is important, too. I buy the best components I can, when I have the money, then when I have collected enough hardware, I start assembling. For me, I enjoy building my own desktop.
One thing I haven't seen mentioned is software, or should I say "bloatware" or trialware. All pc manufacturers include tons of software that most people will never use. That's the main reason I always build my own.
My first PC (circa 1994) was a Packard-Bell (no longer available in the US) with Windows 98, 64 Mb HDD, 32 Mb RAM and all kinds of almost useless software and trialware. Some of the these were kind of cool, but nothing I would have bought if I were building my own. After about a year, I upgraded to 64 Mb RAM, then when the HDD took a dive, I got a 20 Gb, 7200 RPM HDD. The HDD really noticeable decreased the boot time and overall speeded up everything. Huge difference over a 5400 RPM drive. That is also when I discovered that I could remove all of the bloatware included on the recovery CD's.
Sure, I could get a cheap prebuilt PC, then spend a few hours to remove all of the bloatware, maybe upgrade some of the hardware, reconfigure the operating system, and tweak a few things, but what am I saving? I might spend a few more bucks by building my own, but in the end, I get what I want for about the same price, considering the time invested in "rebuilding" the store-bought version.
Since my first store-bought, I have always built my own.
Just my two cents!