Now that you phrase it that way, I guess I prefer a desktop too, because I have most of those things, but split between my NAS in the closet and my laptop docked to my big monitor, keyboard, and mouse.
A previous comment in this thread mentioned QuietPC [0] in a list of prebuilt companies.
They have some really cool fanless builds, that if you were using a CPU like the AMD 4750g [1], you would have zero noise, and it'd make for a very decent workstation.