I wouldn't normally suggest eBay, since you'd have to really trust the seller, but I got the 5,1 12-core in my signature on eBay a month or so ago and it worked out well. Over 2 years of AppleCare warranty left on it (which I verified before purchasing), with 512GB SSD and 24GB RAM, for $3,300.
1) You are locking yourself into older connection standards (USB2, Firewire, SATA, etc), and you are getting older slower MB tech (especially the memory bus)
2) Most of these systems are stripped, so you would still need to buy memory, drives, and video cards.
While it is true that you can get a good system for a lot less, you are NOT getting the horsepower of the new systems. One of the older ones might be good enough, but, in most cases, you are buying a system that is already 3 years old.. and will only get older.