What Tenacious explains is true about switching the power to the multiplexing chip in the Sega controller, you cannot access any of the buttons other than B and C (Fire 1 and Fire 2 respectively) without doing that mod. Usually there is a resistor involved too. Once modified, the pad is functional as a full seven button controller in ADOOM, and can also be used in Flashback and Hired Guns with the Start button and A,B and C. As far as I know, only ADOOM supports buttons X, Y & Z.
A modified Sega control pad doesn't send the same signals as a CD32 pad, so it can't be used as a replacement for these. It can still only be used in games that support 1 and 2 button controllers and specially modified Sega controllers.
You can add support to a game or maybe even a WHDLoad slave if you can program, the instructions are in the ADOOM documentation:
http://aminet.net/package/game/shoot/ADoom-1.4Six button Sega pads should all still work as 2-button pads on Amigas without any modifications. There are some things that stop the second button from working though, such as WHDLoad on an A600. If you play a game from floppy the second button will work, but when using it in the WHDLoad-installed version of the same game the button may wok the first time you press it but never again after that. I don't know what causes this but it's annoying.
As for a list of games supporting two buttons, it would be so long. Someone needs to start a thread with a list in the first post that they can modify and add games to the list each time someone suggests one. Only then will we finally work out a definitive list of 2-button compatible games.
More info can be found in this thread:
http://www.amiga.org/forums/showthread.php?t=50705
