Some machine language games that use the paddle inputs will not work on
the Apple III. The hardware for reading the analog inputs is different, and
some software will not be able to take this into account.
Also, the joystick ports on the back of the Apple III are arranged such
that some games won't work properly in Emulation mode. Most joystick oriented
games will use PDL (0) and PDL (1) for X-Y control. The ports on the Apple III
put these signals on different connectors. Here are the Apple II Emulation Mode
equivalents of the signals available on ports A and B.
pin Port A Port B
4 PDL (0) PDL (1)
5 PB1 PB2
8 PDL (2) PDL (3)
9 PB3