The N64 takes two voltages, on an unmodded system it takes 12v (actually 11v) and 3.3v. On the mobo is a 7805 regulator, so you can take 5v off that too. Basically, you can use LED's which are 3v or 5v, so you don't need resistors; just wire the LED's as you want.
There are a lot of guides and info on the N64 on the Benheck.com forum, have a look.