Nothing, provided you have the necessary exception handlers installed to emulate the missing integer instructions (32x32->64 bit multiply, bitfields and so on).
The 68060 has the bit field instructions. 64 bit integer multiplication and division are missing though. 68020/68030 code is fairly optimal on the 68060 except for branch logic being reversed and the 68060 branch cache will mostly solve that. The larger caches, dual integer units and faster instructions would mean the 68060 could run 68030 code significantly faster (68030@100MHz speed?). The larger caches could cause problems with poorly written code.
