Silver Keys will enable Croc to open Cages that contain either a GobboBaron Dante has imprisoned, or Red Buttons that manipulate a platform or other part to a level. These only appear in Croc: Legend of the Gobbos.
Gold Keys help Croc open Locked Doors that have big, gold locks on them. A Gobbo or something usually important is what usually hides behind these doors. In some levels, the Locked Door is actually the only way to advance and complete the level.