N64, some would say because it is hard to emulate well (we are still seeing somewhat big leaps in it, http://www.libretro.com/index.php/first-ever-revolutionary-n64-vulkan-emulator-coming-soon-only-for-libretro-parallei/
) and it is not the easiest to fiddle with. Personally I would say it is because it has aged horribly, was something of a failure at the time (nowhere but North America really cares about it) and most of the good games for it (the list of which you would probably have space free if you counted on all your digits) have since appeared on other systems which are nicer to play with or appeared on nicer to play with systems at the time -- Resident Evil and Tony Hawk games are great candidates for hacks, why on earth would I do the N64 versions?.http://www.romhacking.net/?page=hacks&genre=&platform=27&game=&category=&perpage=50&title=&author=&hacksearch=Go
Now if you expanded your list to be Mario 64, Goldeneye, Zelda and F-Zero X we might be able to say other than.
PS1, there are many more mods owing to there being many more games. Emulation does not have the best rep and having fought with epsxe plugins at times I can see how that arose, less complex emulators were nice but often lacking in some way too. Also patches can be harder as there were not exactly scene standards at the time, about 10 iso formats in common rotation (nrg, clonecd, standard iso, bin+cue,disc juggler, cdrwin and the list goes on) and you then don't even have the option of dumping your game to bypass it. Many times you can convert and/or go file by file but it is still annoying. It might also be that some of the games have not aged the best but if I am also dealing with the N64 as part of this little exercise then it is not even close.
Poke around some of the trainer sites as well. The PSP's PS1 emulation saw things have a bit of resurgence as well, alas most of it was game specific rather than "look at this site" like you can do for here with 16 bit or various other sites for GBA and DS.
To add to the iso fun then I might also speculate that downloading a 600 meg game is still effort where I might have a complete 16 bit, GBA or older set and downloading a DS game is no big deal either, to say nothing of individual games (give or take some bigger DS ones) is trivial where not so many people host PS1 games.