I work for IT that supports all of the County Goverment's various departments and agencies, about 500 computers. We build most of the computers. It has worked out as big cost savor. Fortunately we setup our volume licence to be transferable because we have used Windows XP and won't transition away from it a department at a time for another year or two. Probally won't compleatly stop using XP until 2014 or 2015. 12+ years for one OS purchase isn't bad.
We don't save much up front, but in the long term to cost are great. Many of the parts have 3 to 5 year warranties. The companies we buy parts have a easy RMA process. We do have a 100 Dells, and I hate jumping through their support idiot's hoops when I have just to replace a dead part.
Dells non-stadard parts make it expensive to repair when out of warranty. More than half of the computers I support are 5 years old or over. There are still a few 8 year old computers!
I had to put a 3 year old Dell out of service, because it would cost $200 to just buy the motherboard on a computer half way though it's life cycle. If it was a custom computer, it would cost $50. I wish we would go all custom computers, but we still buy prebuilt computers for Library Public access computers, for a few reasons. We couldn't build 20+ computers very timley with our small staff already loaded with other tasks, it is harder to put custom built computers into the State and Bill and Melinda Grants paperwork, and the smaller size works better on the Public access desks (Though I guess we could build mini-ITX machines)