I'm afraid not.
Usually the FPGA manufacturers change the pinouts for each FPGA-family. (Such as Spartan -> S2 -> S2E -> S3 -> S3E)
IIRC, if both PQFP-208 parts are compared with each other, 500E Spartan also has more input-only type "IO":s, and the XC3S400 has more INPUT/OUTPUT IO:s.
