Mr. Backup Z64 FAQ

As standart boot cart you should use Super Mario 64 or any other cart with a 4KB eeprom savechip and a 6102/7101 security chip(cic) like Mario Kart 64, Wave Race, Goldeneye.
Together with the bootchip emulation and the country fix you should be able to boot almost every game.

Some games need other boot card to save.

Starwars Episode 1 Racer is needed by the following games, Mario Party 3 doesn't even boot without a 16Kb eeprom boot cart like SW Racer:
Cruis'n World
Donkey Kong 64 (boots and saves with mario 64 if you use z64patch.dat v2.7P or 3.0U)
Excitebike 64
Kobe Bryant in NBA Courtside
Mario Party 3
Mario Tennis
Perfect Dark
Ridge Racer 64
Star Wars Episode 1 Racer
Yoshi's Story

Command & Conquer is needed for:
Command & Conquer
Jet Force Gemini (boots and saves with mario 64 if you use z64patch.dat v2.7P or 3.0U)
Ken Griffey Jr's Slugfest
Legend of Zelda: Majora's Mask (boots and saves with mario 64 if you use z64patch.dat v2.7P or 3.0U)
Megaman 64
NBA Courtside 2 featuring Kobe Bryant
Pokémon Puzzle League
Pokémon Snap
Pokémon Stadium
Starcraft 64
Tigger's Honey Hunt

Be aware that you can only save on game's savegame on a single cart. To save more than one game you need multiple save carts.

Some alternatives:
Flashram und 6102:
Command & Conquer
Megaman 64
NBA Courtside 2 Featuring Kobe Bryant
Pokémon Puzzle League
Starcraft 64
Tigger's Honey Hunt
WWF: No Mercy

16Kbit eeprom & 6102:
Mario Tennis
Ridge Racer
Starwars Racer

Games with special protection:
Banjo Tooie - needs Perfect Dark or Donkey Kong 64 as boot cart and therefor needs to be started without the help of the OSD.