Worrying times, it really makes you think twice about investing hundreds of hours into a fan game only for it to be slapped with a take down notice. From the looks of that list it seems 42 Zelda games were taken down.
Right now I'm only working on Zelda mini games so that if they do get a DMCA request I won't feel too bad as I won't have spent too long on it. For those who have spent literally years
developing their game, ouch
I was thinking this morning about the possibility of making fan games using the same mechanics and gameplay as they were intending, but with all copyrighted resources such as graphics, trademarked names, sounds, .obj etc files files replaced with 'placeholder' resources when releasing the game for download, the sort of things you find on opengameart.org.
There would then be another website that hosts resource packs that contain the more sensitive
materials, the user downloads the pack for the game they are playing and replaces the /resources/ folder and voila, you have a Zelda fan game!
EDIT: Another thought, for a place like ZFGC where we tend to use the same graphics it might be the case that you can create 'universal' resource packs that can be used across multiple games easily. Lets say you are making a game using ALTTP graphics and sounds. You use the resource pack when designing the game, release the game using placeholder graphics and text e.g. 'The Large End of Zoldo - The Shattered Orb'. You simply state at the top of your post that if you want
to have Zelda graphics you should download the ALTTP resource pack from a place you have no knowledge of
and add it to the game folders.
Then Nintendo can't issue a DMCA notice for your game because if you have been thorough there are no infringing materials you have created.