I'm looking for a (low-cost) spartan 3 based board, containing a low to medium sized spartan 3 fpga, two 100 MSPS 12 bit AD converters, and ideally also one or two 8-12 bit DA converters, but I didn't find any.
100 MSPS @ 12 bits is a little out of the ordinary for a low-cost FPGA board. I'd suggest looking for an FPGA board with sufficient I/O connections and cobble the system together with an A/D converter board (if you can find that - perhaps an evaluation module from the converter manufacturer?).
Something in this vein is our Broaddown2 product which we have been using with a high performance Linear Tech ADC eval module recently. The eval module we have been playing with nearly straight plugs into our edge connector on this poduct.
Details of BD2 here
With some lashing up quite of a number of our products could used with eval modules from the likes of Linear Tech. We have lots of uncommitted pins and bank voltage selection in various of our products.
Longer term we may have a product, maybe more, that meets your entire requirements but I can't possibly talk about these quite yet.