Pinocchio's singing voice during the "'IL Colosso" song was provided by Brian May, only his vocals were sped up to match Jonathan Taylor Thomas's voice and the soundtrack credits "Just William' as Pinocchio's singing voice.
Wallace Shawn was originally set to voice Pepe but was taken over by David Doyle, though the trailer for the film features Pepe with Shawn's voice and Shawn is even credited in the trailer.