I've been thinking a lot about a sixth board to support an FPGA to assist in debugging and emulating the rest of a complete system (like a Busicom calculator). I'll still put a connector on the I/O & Timing board so the CPU can be interfaced directly to external logic, but having the ability to access inter-board signals and emulate missing parts of the CPU seems worth the effort.
When I first started this project, I used a Xilinx Spartan-3E FPGA development board for this, but it only provided 40 I/O signals. I thought about building my own board with the same FPGA, but it seemed a bit pricey and complicated to interface (three supply voltages with rigid power-up timings, etc). Thus I looked around and found the Lattice iCE40-HX series.
In the years since I started this project, the FPGA world has changed. Xilinx came out with their Spartan-6 series, which can run with two voltage supplies without stringent order or rise-time criteria. The parts have also become denser and cheaper ($16 vs $22). The iCE40-HX4K is still a bit less than half that price ($7), but when considering the cost of the PCB and the components required to support the FPGA (voltage regulators, SPI Flash ROM, level-shifting FETs) the difference in the cost of the FPGAs is noise.
I've decided to use the Xilinx Spartan-6 LX9 (144-pin TQFP) rather than the iCE40-HX4K. Why? In a word: Tools. I'm much more familiar with the Xilinx tool chain, and the iSIM simulator runs under Linux. The Aldec simulator provided by Lattice is a fine tool, but it only runs under Windows.
I need to finish pinning out all four remaining boards before I lay out the debug board, but I'm almost finished creating the Eagle library parts I'll use, and have most of the other components selected.