Yeah don't go pre-built. You might find that people like Circuit City and Best Buy will send you things in the mail with great looking pc deals.
It might be great looking at a pc with a Core 2 Duo and 2GB DDR2 RAM, but it comes with alot of downfalls when buying from them:
It's nearly unheard of to find better CPUs in these systems than e6400 and a AMD 4200+
The DDR2 RAM is probably only 667 and won't overclock for anything
The mobo is probably bottom-of-the-line Intel or AMD and won't overclock either
There are no video cards worth mentioning in these machines, so that is at least another $300 for a highish end card to go in there too
The rigs are not customizing-friendly. If you want beefier hardware, it usually means you'd end up replacing more than one part to compliment the one you would want. aka replacing the PSU for bigger hardware, or psu for mobo. Also, if you put in new stuff, you can bet your internals will get too hot because those towers are already too small and have next to no airflow.
If you altered anything, there goes your warranty too.
You still might find a rig for $700 in the ads for these stores, but then you will see a price tag of $1100 because you'd have to send in 5 different mail-in-rebates to get the money saved.
So just build your own. You don't have to spend alot of money either. Whatever part you get from newegg will be alot better quality wise than the equivalent that a place like Dell or HP would send you.