I don't know the data transfer rates of SD cards, but this might affect your choice. Chances are though, you'll get the best rates if you distribute cards across your built in busses. Since you'll need a USB for your keyboard and mouse (unless you use bluetooth), you might be wiser to use firewire readers. 7 on each port daisy chained together.
I like this idea. You should build a mini Xserve case for it too. If you disassemble the Mini and lay the optical and hard drives nect to the logic board, you should end up with a 1U server the size of a switch or hub.
When the Mini first came out, I dreamed of getting several of them and installing the logic boards in a 1U server case........
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