I've played around in the past of the 2D Flash fan-made version of the popular Valve game Portal. It has basically the exact same mechanics, but as a 2D side-view flash game.
Lately I've toyed around with creating a simplified flash version of some of my favorite franchises (such as Zelda, Mario, Splinter Cell, etc.). Of course, nothing is "stopping" me from just using the same mechanics and just changing the name to something not copyrighted.
I have witnessed projects that have tried to directly port a 3D game into a 2D simplified version, with the exact same plot and puzzles (Ocarina of Time in 2D comes to mind), and I have seen them being shut down. But I am not likely going to exactly duplicate any game...just borrow some of the source material and basic underlying mechanics.
For example, if I were to make a Zelda-influenced fan game, I would have items such as the Hookshot, Boomerang, and all other sorts of ones from the Gameboy Zeldas; just with a custom plot and dungeons. With likely the same mechanics.
What are the legal issues involved in this? I used to think it was a "Don't do this ever; it's a bad idea."
But then I've seen the Portal clone, and now I'm curious.