Building my own PC had nothing to do with cost.  When I first built a PC ~4 years ago, there was a price advantage to building yourself.  Now, however, if you're concerned primarily about cost there are lots of low-cost solutions.  The PC market has gotten too competitive to expect to save anything by building your own.
The advantages I see, however, are:
- Complete control over your PC.  You get to choose everything.  Want a BX board instead of a VIA?  No problem.  How about a GF2 GTS, but you don't want to pay retail prices?  No problem.  Want IDE RAID?  No problem.  I know every single piece of hardware in my computer, & chose every single component myself.
- Easy availability of drivers.  It's easy to find drivers for a SB Live! value, but it's a pain in the ass to go look up your PC on IBM's web page, & download their POS proprietary drivers.  Everything in my system is standard, & I can download all the drivers I need to completely re-build my system in 1/2 hour, even on 56K dial up.
- No extraneous crap on your PC.  Don't want the "1,001 titles" that come with a retail PC?  No problem.  You install Windows from scratch, & then install only what you want.
- Raw speed.  I guarantee you my system will out-perform virtually any pre-built system.  I've tweaked the hell out of it, & it shows.
- Best of all, experience.  I don't need to call tech support to fix my computer, I can tear it apart & re-build it any time I need to.  Power supply fails?  It's a 20 minute drive to pick up a 400W ATX P/S, & maybe 20 minutes to install it.
I will NEVER buy a pre-built system.
Viper GTS