Certain emulators will let you play with a mouse. From memory here I'm thinking FCEUX and RockNES . I though Jnes did too?
And if you have a CRT you can get any usb gun to use with it. LCD's and Plasmas need a special gun(not as good).FCE Ultra is an open-source, portable NES/Famicom emulator based on Bero's FCE source code. It has excellent sound emulation and support for a wide variety of in-cart expansion hardware("mappers"). PPU/CPU timing is good(in comparison to *most* other NES emulators, which are rated poor in this area). Several VS Unisystem games are supported well. Interesting features include emulation of the Zapper and VS Unisystem light gun via the mouse, and "authentic" Game Genie emulation.