Yep I also think FPGA solutions and Classic hardware could go very well together.
I think it's more likely that the old hardware will end up getting replaced altogether. What if this hardware existed for about 300 euros (~$400 AUD or U.S.)?
Cyclone 5 with 68k+@150MHz + 512k L2 cache
1 GB DDR3 memory
HDMI (includes sound)
2xPCIe
2xSATA
Gigabit Ethernet
USB2
1xCF
PS2 keyboard and mouse
2x9 pin joystick ports
Ok, your 68060 can compete with this but what if we can double the CPU speed for say 3x the cost and in about a year a 500MHz+ enhanced 68k CPU could be possible with the hardware specs above still at 3x the cost. It probably wouldn't fit in your 1200 but it should fit in a mini-tower of some kind. Would you be persuaded to give up your old 1200?
What I'd really like to see is some FGPA projects that have an (open source) active developer community behind them to continually improve the performance.
An upgrade path and an active developer community are key to all the fpga projects. The more open projects will attract more developers.