The 12.x tool still supports the .exo file formatting and programming, but you will need to use the command line instead of the GUI.
To generate a .exo file, use the "-p exo" option in PROMGen.
For example, (assuming the target device is XCF32P):
promgen -p exo -u 0 my_design.bit -x xcf32p
To program a .exo file into a PROM, use iMPACT batch mode.
For example, (assuming the PROM is the first device in the JTAG chain) after entering iMPACT batch mode, run the following commands:
setcable -port auto
assignfile -p 1 -file my_design.exo
program -p 1 -e -v