Patch files for Super Mario 64 ROM hacks usually come in one two forms: BPS or PPF.

BPS is an efficient, generic binary patch format. It supports delta-encoding, folder patching, infinite file sizes and checksum verification.

• Floating IPS (Windows,Linux) - create and apply IPS and BPS patches
• JavaScript IPS/BPS Patcher - JS version of Floating IPS
• beat (Windows) - create and apply BPS patches

PPF (PlayStation Patch Format) is generic binary patch format. While inferior to BPS, it's the most common patch format used for older SM64 hacks.

• PPF-Studio (Windows) - create PPF patches
• PPF-O-Matic (Windows) - apply PPF patches
• applyppf (Windows,Mac,Linux) - command line tool to apply PPF patches

• http://www.smwcentral.net/?p=viewthread&t=73147
• http://www.smspower.org/Hacks/HowToUseBPSAndIPSPatchFiles
• http://www.smwcentral.net/?p=viewthread&t=78938