I have generic noname USB gamepad.
It works in windows (win7 64) and in other games that support gamepad.

It even works when mapping snes9x 1.51 controls but it wont work when I enter game...
I have also tried with snes9x 1.53, no luck.

Any suggestions, ideas?
Or I have to buy Logitech gamepad?

Is input set to "Use SNES Joypad(s)"? Is the Joypad enabled (in the input configuration)? Does it work with bound keyboard buttons?

Yes, yes and yes.

I just tried to disable nod32 and still no effect.
I have also tried compatibility mode xp sp3, vista, run as administrator.

Could you upload your snes9x.conf file somewhere?

You've mapped your controller to Joypad 3 - is that what you want? You have to use Joypad 1 for normal SNES games.

If you indeed want to use it as Joypad 3 (eg. for player 3 in Bomberman) you'll have to select "Use Super Multitap (5-Player)", otherwise only two Joypads will be used.

Unbelievable! Thank you! As Joypad 1 it's working!

I already tried VirtuaNES and there controller 3 is working as gamepad, strange?

Anyway, thank you again and I hope it will help others too

The "Joypads" in Snes9x represent the real SNES joypads. So joypad 1 is the one in the left controller port, joypad 2 is the on on the right, and later ones are those plugged into a multitap. If you map your gamepad to joypad 3, it is now one of those plugged into the multitap - thus most snes games do not react to its button presses.

I'm finding a very similar problem; I'm using a 360 gamepad, and I've configured it in Snes9x as pad 1. Configuration works fine - but it doesn't seem to have any effect at all in game.

Any idea how to make it go?

I also have a Xbox360 controller and the solution above didn't work BUT the problem was quite similar. The exact opposite to be more precise
Map the buttons of gamepad 3 instead of gamepad 1.