Hi!
I was successful in the past using xc3sprog to program Spartan3 (50,
200) and the associated serial flash. Can anyone say something about xc3sprog and Spartan3E and Spartan3A devices? A quick scan in the devlist.txt shows no E/A device but that does not mean it won't work. I don't have any board with this devices to do the test.
To xilinx: The tools for CPLD/FPGA programming should be /user land/ and /open source/. I do not care about fancy stuff like ChipScope, keep that proprietary if you need to.