I just purchased a new Mac mini Server, the base configuration, for testing an upcoming version of SoftRAID. Just out of curiosity, I thought I would compare it to my main desktop machine, an 8 core MacPro4,1 2.26 GHz. In every test I could think of, the Mac mini Server was as fast or faster than my Mac Pro. I even tried transcoding a movie with HandBrake, my usual test of a processor intensive operation and the Mac mini with 4 cores was the same speed as the older Mac Pro was with 8.
I'm sure a more recent Mac Pro might be faster, but I'm not sure by how much.
The only thing which makes me reluctant to move to a Mac mini is the difficulty of replacing the disks.