A good way to give something the appearance of 3D is by making a 3D model in a 3D modeling program, such as SketchUp, taking screenshots at different angles, and putting them in your Scratch project. This is especially good for First Person Shooter style sprites, check my account to see some things I've done with this. Another really cool 3D game was made by someone else, here: http://www.scratch.mit.edu/ext/youtube/?v=PBwAsGIL6MU (the gun you see was actually made by me, but he did the rest of the 3D environment.) I don't know. Just some interesting stuff.
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