Would love for the ability to Load any of the Hacks. Missing Stars and SM64 (2) would be awesome
Depending upon what the hacks do that can get tricky. It is certainly not going to just be a matter of finding the new address and decrypting or decompressing a ROM like it might have been for the various official emulated versions or other N64 emulators people are injecting things into.
If they are just assets then chances are it can be ported out, or maybe remade, in reasonably short order as these things often still want the original assets to build the code. Might even be reasonably doable (especially as we technically have the source code to the ROM) to make a tool that is aware of things to know where something else exists now -- we have seen a few things like this before (pokemon tools often will read all the various pointers down the line to find something that has been relocated, and atrius' golden sun tools also provide an example of some more content aware stuff) so it is not unbroken ground. The further the hacks get from the original ROM in terms of general overview (as in the stages can be entirely new but if it is still the original notion of 15 stages going off similar layout to the original ROM then that is not much of a change for this sort of analysis) then the harder this gets (Someone starts expanding this to dozens of levels beyond what the original had and that gets trickier by far. I don't have the most experience with Mario 64 hacks but I have seen what I consider amazing hacks do things that would be fairly minimal changes to the ROM, and have seen new kids rock up and play with a GUI editor to in turn radically change things despite the end result being junk and also not that apparent in normal play. Good hackers making good hacks have good reason to make radical changes as well though, and it is far from unexpected for such a thing to happen.).
If the hacks start messing with code (different jumps, functionality and what have you, like I have seen a few go in for) then that gets far harder again -- any such hack made before this likely was an assembly hack laid on top of the original and thus won't likely decompile to anything useful. You would then have to figure out what the assembly tweaks did and port or remake it accordingly in the source code. Now you do have the added bonus that you can probably map the source code to the resulting parts of the ROM (indeed if the statement from the people making the decompilation is anything to go by this was the original intent of such a thing).
Short version. I would probably start this sort of thing off by building essentially the ultimate Mario 64 hacking tool. Something that starts at the very heart of the ROM and with an awareness of all the general pointer layouts from the start right through to general 3d models and locations of any binary code (this tends to be moved far less by hackers as it is a nightmare and gains little). Having the original ROM's source code will help here as well as you know you will not be missing anything.
With that you will know what is where and what is changed.
It will also want to do a comparison with the original ROM to see what is changed in general for the binary (as in what the CPU runs, not the whole ROM) and then alert you to do any further analysis.
It will however also be useful for anyone looking to smoosh together hacked ROMs in general, cut things down to run on say the Wii emulator, port them out to source ports, possibly some of the speedrun/TAS/romhack speedrun set, and possibly also those seeking to make them in the first place (assuming people are going to continue making "traditional" mario 64 hacks at this point).
If you can program (literally any language that can read files and manipulate them should do here) then if you skip any 3d viewers, sound playback, 3d editors or general graphics editors it is not the hardest thing; it is little more than a very crude database or archive unpacking program.
edit.
Forgot to note. Now N64 hackers still working on the N64 have source code to play with that might make creating an "ultimate" tool even harder still. However said ultimate tool will work for both the base ROM and likely any hacks made the "traditional" ROM hacker way.