So, I know not all of these are realistic, so I'll seperate them into categories. Ones I think would be easy to port, ones that I feel be moderately difficult to port, and ones that are likely wildly unfeasible to port. Keep in mind I'm not a porting expert, so these categories may be inaccurate.
I initially meant to provide in-depth explanations of why I wanted each of these, but I ran out of steam after finishing the "wildly unrealistic" category, so not all of the hacks in the "easy to port" and "difficult to port" categories will have explanations. My apologies.
Easy to Port
SM64: The Missing Stars - The first major hack of SM64, which I hope is enough reason for it being on this list.
Mario Party 64 - I just really, really like this hack. It's a very fun reimagining of Mario Party 1 and its boards.
Kaizo Mario 64 - I know much, much better kaizo hacks have come out since this one. I know it's not the best. But I just have so much nostalgia for this one. I used to watch videos about it all the time when I was a young kid. And I feel like it'd be cool to play it with friends.
Wario's Hint Art - I feel like the actual game of this one would be very easy to port. It'd be the hint art itself that'd be the hardest part, since it's contained in a google drive link. Maybe the hint art images could be added to the pause menu somehow?
Star Revenge 2 Act 1: To The Moon - One of the Star Revenges that hasn't been ported yet. Which, by the way, props to whoever's been porting a bunch of the Star Revenge hacks! You're awesome!
Ztar Attack 1 2 and 3 - Cool hacks that a lot of people like.
Shining Stars 2 3 and 4 - More cool hacks that a lot of people like.
Green Comet Hacks (In General) - I'm lumping all these into one since the premises are all the same. Either vanilla Mario 64, or a romhack of it, but all the stars are hidden in different places now! While I understand why a bunch of people didn't like this in Super Mario Galaxy 2, I think it'd be much more fun in multiplayer, with a bunch of players all scouring every level to find the hidden green stars. And, since the only major thing different in these hacks compared to their counterparts is the star placements, I feel like they'd be very easy to port, as long as their counterpart has already been ported. I feel like, out of all the hacks on this list that aren't in the "wildly unfeasible" category, these would be the most enhanced by multiplayer.
Difficult to Port
Peach's Fury - I think this one would be really fun in multiplayer! One huge level that everyone scours together for the stars.
Mario's Vacation Course - Same reasons as Peach's Fury, though I feel like this'd be a fair bit more difficult to port, due to the moveset unlocking stuff. Probably not impossible to port, but I wouldn't hold my breath for it.
SM64 Decades Later - This is my most wanted out of the hacks not in the "wildly unrealistic" category. I just think it'd be so much fun to run around this one with friends!
Star Revenge 0: Galaxy of Origins - One of the Star Revenges that hasn't been ported yet. Also I just really like its name.
Star Revenge 8: Scepter of Hope - One of the Star Revenges that hasn't been ported yet. Though I haven't played this one yet, I think it's more Touhou-heavy than the other Star Revenges.
Star Revenge 6.25: Luigi's Adventure DX - While its original version was ported, this remake has not been ported.
Another Mario Adventure - Another hack I think is pretty cool. Though also another that'd probably be difficult to port.
Super Mario and the Monstrous Manor - I have no idea how Co-op DX handles 0-star hacks, but I'm gonna guess the answer is "not very well", especially for a hack like this. It's a really cool hack, but I just don't know how a bunch of the stuff in it would be ported.
Beyond the Cursed Mirror - I haven't actually played this hack myself yet, but I've heard glowing praise for it, to the point that assets from it made it into Mario Builder 64! It'd be really cool to see it get a port, but given all its custom stuff, I think it'd also be pretty difficult to port it.
Wildly Unrealistic Dreams
Mario vs. Wario Ware - I feel like this would be flat-out impossible for multiplayer without major alterations, but if it was possible, it'd be so much fun. Multiplayer is a staple of Warioware, and from what I've seen, it's a chaotically fun time. But, again, I don't think this is feasible without major alterations, and even then, it'd likely be a lot of effort.
Bingo 64 - As this one makes use of the main menu of SM64, I feel like it'd be very difficult to port without major alterations to SM64, not to mention the custom UI. I do think it'd be really fun with multiplayer. Imagine two people racing each other to get the same bingo objective because it's on both of their cards! Unfortunately, though, I feel like the likelihood of this being ported is the same as the probability of winning big at bingo.
Mario in the Multiverse - People have already mentioned this one in this thread, and while I agree it'd be really fun to see it in multiplayer form...I don't think it's feasible. With all the custom mechanics, unlockables, and even a functional shop, I feel like it'd shatter like E. Gadd's machine if we brought multiplayer into the equation. Maybe in another universe.
Serene Fusion - One of the most highly regarded romhacks of all time. Starting as a remake of Super Mario 74, it became so much more, and it would be an absolute blast to play it with a bunch of others. Unfortunately, I feel like the banana peel alone would be impossible in multiplayer, to say nothing of the rest of this gorgeous hack. I do wish it was possible, but I just don't think it is.
Kamek's Volcano - One of, if not the best first hacks, Kamek's Volcano is a masterpiece...or so I've been told, I haven't actually seen much of it yet. What I have seen, though, while really really cool, also seems really really difficult to port.
SM64 Ocarina of Time - One of the first hacks to bring a different style of gameplay to SM64, this one makes it play more like a Zelda game, even including the setting of Ocarina of Time, while still retaining a lot of Mario 64. It's awesome to play, but also its Zelda-like gameplay mechanics seem like they'd make it very difficult to successfully port.
Super Mario 64 Land - Another hack that tries to convert Mario 64 to be like a different game, this one opts to go for another Mario game, particularly Super Mario 3D Land. While very fun and cool, and 3D World multiplayer is so, so much fun, I feel like the overworld alone would make it difficult to port, to say nothing of the levels themselves. I'd wait for Super Mario 64 World.
Through the Ages - I admittedly don't know a lot about this one either, but judging by most of Kaze's other major hacks being in this category, I don't think we're porting this for at least a few more ages.
Mario Builder 64 - Do I even need to explain why this one is in the "wildly unrealistic" category? I'll do it anyways. Mario Builder 64 allows you to create your own custom Mario 64 levels, share them with others, and play other people's levels! Imagine going through the catalogue with your friends, or even building a level together! Unfortunately, there's so, so many hurdles to port it, from being able to pull from the Mario Builder 64 level database, to how level creation would work in multiplayer, to the entire UI. I sadly don't think this one is portable at all.
Last Impact - You all knew this one would be in this category. Quite possibly the most famously complex Mario 64 hack, it featured more custom content than any other hack of the era. Unfortunately, this also makes it seem near impossible to port. Full cutscenes, cinematic boss fights, minigames, it's a lot of really cool stuff! But, like I keep saying in this category, I don't think it's portable, at least not any time soon.
Sorry for all the text for my very first post, but I hope you all enjoyed reading it!