the $200 works out more like $250 in the UK. Doing it myself, I would probably also add a 250GB SSD instead of the 1TB drive (changing this on the apple store costs about $200, while I can buy a samsung SSD for significantly less than this). Comparing the DIY option to a factory build, when one includes the SSD starts to make a much bigger difference.
i am intending to use the SSD as a boot and web folder drive, I will partition the 1TB to a 250GB bootable mirror of the main drive and the rest as a 'whatever' drive. I will also be chaining some SATA drives on thunderbolt.
I will be installing server, the intention is that this will eventually replace my MDD that has been running leopard server for many years. I will actually build the mini into the G4 case one day.
I will have another look at the tear downs, I noticed the new one still had the second sata port but couldn't work out if cable routing etc was the same.