1: In 90% of the N64 games, you will find that the "L" button is an optional button. Like in Mario 64, the L/R button work with the camera view. In The Legend of Zelda - Ocarina of Time, the L button is for the map, and the R button is for the shield. Z-Trigger is used for a function called "Z-Targetting" which puts little yellow triangles around your target and lets you "lock on" to that target until you click it again. However, in some games like Golden Eye, the Z-Trigger is a firing/attacking button. (It fires your gun in 007) and in some games, it is used to block. So you might want to test around in the individual games to see which games NEED the real L-button and which don't. Those that don't? Just use Button 9 for that. I WOULD have kept them on L5/R6 if not for Z-Trigger being more needed in the Analog/Thumbstick games.
2: The most notable games that require the C-Buttons are the Zelda games (for items to be used) and are sometimes used for "Strife" (007 uses this in which the C-Left/Right move you left/right while C-Up/Down aims your gun up and down). I haven't much experience in the fighting games for N64, as I only got mine (the real one) for the two Zeldas. But there ARE some that require the keys to be pushed in exactly. In Ocarina of time for instance, you have to play songs with the C-buttons...
3: The songs I was refering to were a key feature in Ocarina of Time and Majora's Mask. For instance, you could cause it to go from day to night by playing C-Right, C-Down and C-Up. And while you can do that easily enough with the right-analog stick... can you imagine trying to do the "Bolero of fire" with the stick, with the key sequence being "C-Down, A, C-Down, A, C-Right, C-Down, C-Right, C-Down"? Not easy. Which is what I was talking about. But it IS nice to have the stick for the songs ~anyway~ for the easier ones. Plus as I was saying with Golden Eye, if you have the Left-Stick for controlling your movements in the game, and your Right-Stick for the strife function, then you can move WAY easily. And you can always use your left finger to fire your gun.
Hope that explains a few things.