For SNES (if you're using the RGR Plugin) the controls can only be changed if you are able to click the button Set Keys in the ZSNES menu, if you are unable to click due to the mouse pointer not responding these are some possible solutions:

- Try these solutions in a different internet browser if they don't work in your current (Chrome seems to be the worst case for this bug and Firefox seems to be more compatible):

- While the menu is open, go to full-screen (non-windowed) by pressing the keys Alt and Enter simultaneously, or go to CONFIG with the arrow keys and select VIDEO from the list with the Enter key, then select another resolution that will fit your monitor, but doesn't contain "W" (windowed).

- Click on any page within the browser that you're playing the game on. The game's page for example. That will bring the page on top of the game window. Then click on the game's tab in your taskbar. That will bring the game back to the top page. After you've done this, move your mouse up to the game and it should line it up with the menu cursor, if not, try clicking on the menu.
If this fails, try either of the combinations of the keys Alt + Esc then Alt + Esc again, or Alt + Tab then Alt + Tab again (which will do the same process)

- MouseKeys may work for movement of the pointer with the keys, or it may enable movement with the actual mouse after you've pressed the key for left-click:
Instructions for this -

Windows 7 - http://windows.microsoft.com/en-US/windows7/Use-Mouse-Keys-to-move-the-mouse-pointer

Vista - http://www.microsoft.com/enable/training/windowsvista/mousekeys.aspx
(I'm not sure of which key for left-click)

XP - http://www.microsoft.com/enable/training/windowsxp/mousekeys.aspx

To click by using MouseKeys in XP - http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/access_mousekeys_howtoclick.mspx?mfr=true
(You may have to press 0 on the Numpad after clicking with MouseKeys)