They might be easter eggs or remainders of some earlier version of the game, but these things are hidden, and you can find them. First, there's the hidden toy train in Super Mario Galaxy: in the first mission of Toy Time Galaxy, proceed until the first Spring Mushroom, but don't get it. Scale the next ledge using wall jumps, then at the second Spring Mushroom, take the conveyor belt to the right and jump onto the orange block. The train is under the ramp, use first-person view to see it.
An interesting, but easily missed easter egg in Super Paper Mario can be found in one of Francis's rooms in Chapter 3-4. Just take the middle door in the hallway with the paintings and ride the elevator up to the room with the MeowMaid. On the wall behind the chest will be several Nintendo consoles, and you might need to walk around a bit in 3D mode to make the camera show all of them.