All these sites that sell machines like that, they're mostly off the shelf parts. It's not hard to put together a massivly powerful computer.
It IS costly, but not nearly as much as they charge for one of their ubersystems.
Tyan makes motherboards that will accept 8 AMD 64 bit opteron CPUs. You can get dual core opterons for an effective total of 16 CPUs. Now each CPU socket also has it's own memory slots, which would give you a maximum of 64 gigabytes of DDR memory. Raid together a pair of 500 gig hard drives for 1 TB of storage, raid together 4 for 2 TB, etc.
[This message has been edited by Jax184 (edited 04-06-2006).]