Consider adding a few extra pieces of hardware that are missing from existing FPGA mining systems in order to allow it to operate in standalone mode.  I'm talking only about some SRAM, and ethernet port, and an SD slot.  The purpose of these additions is to allow the FPGA to run Linux via a soft-processor on board.  I'm assuming you're already planning to include some flash memory to hold the bitstream so that the device can coldstart by itself.

I have used just such an approach on my Altera DE2-70 development board.  It runs no-mmu uClinux on a Nios II soft processor.  Both the Nios II and a slightly modified version of fpgaminer's FPGA mining code are loaded into the bitstream.  I've nearly completed a very simple C-based miner (no-mmu uClinux is too limited for existing miners as far as I can see).  It communicates directly with mining pools via JSON/HTTP in order to fetch work and report results.  It is all somewhat preliminary at this point, but I hope to have a fully functional system running within a week or so (albeit at a measly 25MH/s which is all I can squeeze from the DE2-70).

It should also be straightforward to get uClinux running with an MMU on an FPGA which creates a lot of flexibility and opens up a lot of possibilities in terms of customizing the system.  For example, a tiny web server could be run in order to allow the user to control and configure the system (just as is done on many consumer grade wireless routers).  In fact I will probably do this myself as soon as I finish with the no-mmu system.  BTW, uClinux runs on the Xilinx MicroBlaze soft-CPU as well.

If this is of interest and if you'd like some assistance creating it, let me know.