It's worth it, just probably at that low of a price because of the need to buy an OS with it.
The reason why it's good to build your own is not only because of the money saved, which isn't much at the lower price ranges, but because of a number of other factors.
First, you get to pick out everything. That means you get exactly what you need out of the build. You don't waste money on having to buy a more expensive configuration just to get a faster CPU or more storage space.
Second, you make sure you get the highest quality parts. Prebuilt vendors cut corners where ever they can. If they don't have to advertise the part (the CPU, GPU), then it'll be the cheapest, lowest quality part they can find. You'll get slow RAM, cheap motherboards, tiny and low qualtiy PSUs, slow HDDs and flimsy cases with poor cooling. If you build it yourself, you're ensuring you get quality parts.
Third, you get to know everything about the computer. You know exactly what isn't working properly and how to tweak it to get the most out of it. You know what the build can handle. You know exactly what you can use to upgrade it.
Finally, there's the satisfaction that you built it yourself. It's not something you just bought.
You can't beat them in price below the $600 level. HP and Dell buy the parts directly from the manufacturers cutting out redistributors and store fronts and e-tailers (like NewEgg). I read in the book The World Is Flat how Dell does this.
However, you can get fairly close to the price, get better quality parts, and leave yourself the option to upgrade it later. You can get a case that can fit a graphics card and a better power supply that can power it. You will likely have to replace the power supply in a Dell or HP PC that comes with integrated graphics, and that presumes the case uses a standard ATX power supply and the card will fit in their case.
Depends on exactly what your intentions are. If you don't give a crap about upgradability with this project and just need typical tasks you can create a frankenputer from stuff on ebay and criagslist. Esp if what you're replacing is a single core or this is the first thing.
A nice regular AM2 mobo plus any dual core athlon 64 would do fine most likely. Doing it that way would probably be more like $200-250.
The parts MadAdmiral listed are very good for less than $400 and as stated is upgradeable. Only downside is if a part does go bad you have to send it in for warranty replacement vs calling Dell or HP. Build-it-yourself doesn't have the extra lite programs that annoy you to upgrade or want to be the default software for a particular file type.
I'd add a $30 drive bay card reader if you need it.
In my book your downside is an upside. Those OEM's typically only have a 1-year warranty. While most of the parts themselves would otherwise enjoy a 2-5 year warranty. Sure you have to not suck and be able to figure out which thing is giving you trouble, but you'll most likely be getting a free replacement. If it's outside, then you can get a cheap replacement, without worrying that it's possibly proprietary and that you won't be able to do anything about it.