Firstly, it's cool and all that you built your own boxes... that's a great way to go if you can (ie you have the time and expertise to support the group when things go wrong) but it isn't really relevant to the discussion about the price of OEM workstations (that come with warranties and support, etc). Your group might not need that stuff, but for people that do, building it yourself isn't an option. Not to dog on you or anything... just that different groups have different needs.
Ok... with that out of the way... I'm _not_ off base on the price.
Go here:
http://boxxtech.com/products/3DBOXX/8550.asp?prodid=8550
Click "Configure a Boxx System"... put in your email.
Select the "WS DUAL XEON X5650 2.66GHz, 12MB cache, 1333 MHz, 6.4 GT/s QPI (Six-Core) " processor (because that's what the starting Dual-core Mac Pro has in it).
Click Update Total: $6,659.00
Now go here: http://store.apple.com/us/configure/Z0M4?
Select 12GB of RAM. Total: $5,449.00
Now. There are some inequities (graphics cards aren't the same, better HD in the Boxx workstation, etc).... but it's pretty clear that Apple isn't "Overpriced".
Why do we have to keep discussing this every single damn time Mac Pros are brought up???
If you don't want to assemble your own workstations and you really do need WORKSTATION class components... a Mac Pro is a great workstation and falls in line with all the other high-end workstations on the market in terms of price.