So how ARE you supposed to hold an N64 controller?
The truthful answer is that no game ever requires you to hold more than two prongs at a time. A sidescroller like
Mischief Makers requires you to hold the outer two prongs, using the D-pad to move and the face buttons to jump and attack, while the control stick goes completely unused. A 3D game like
Super Mario 64 or
Ocarina of Time has you hold the center and right prongs, using the control stick to move, Z shoulder button (underneath the center prong), face buttons, and R shoulder button, while the L shoulder and D-pad are never used. A first person shooter like
Golden Eye allows you to hold the center prong with either hand, while holding either the left or right prong with your other hand, using the Z shoulder button to shoot, the control stick to aim, while the D-pad and C buttons both move your character.
Fun fact, the Nintendo Wii Nunchuck uses a modified version of the mold used to create the center prong, so the N64's controller is more comfortable to hold than you'd think.