cylum's snes rom set
Nintendo Roms V.2
This is a new list I made because links in the last one went down. The Wii archive.org collection has mostly everything but G8 (the last characters in the url)
has everything. The gamecube links downloads reasonably fast.
 
Switch Roms
https://drive.google.com/drive/folders/1VAxbSUcVindLxf9pVWvh64B-0Q8aM6xZ

Wii U
https://pastebin.com/BEXvv6Jc My own personal list

Wii
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https://archive.org/details/RedumpNintendoWiiAmericaPart1
https://archive.org/details/RedumpNintendoWiiAmericaPart2
https://archive.org/details/RedumpNintendoWiiAmericaPart3
https://archive.org/details/RedumpNintendoWiiAmericaPart3_201802
https://archive.org/details/RedumpNintendoWiiAmericaPart5

The Metroid Prime Trilogy works perfectly from these links.

Anything from these links needs this program to turn the .dec files into ISOs
https://archive.org/details/nNASOS1.8
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Download the zip of the files and extract the files into a folder, to extract a rom drag the rom onto the .exe
the command prompt should popup and extract the ISO from the .dec file. I assume mac and Linux are similar but I don't
have PCs with either to be able to test.

Missing a part 6 no Xenoblade Chronicles... G8 can be used for that so not a big deal

Wii Scrubbed ISOs
https://drive.google.com/drive/folders/0B7H6hIZDxNXeQW9uODA5UkM0ZG8

Gamecube
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https://archive.org/details/RedumpNintendoGameCubeAmerica
https://archive.org/details/RedumpNintendoGameCubeAmericaPart2
https://archive.org/details/RedumpNintendoGameCubeAmericaPart3

3DS
http://www.3dsiso.com Requires a login but by far the best rom site for 3DS games.

3DS Virtual Console
https://mega.nz/#F!yLBiwApZ!JlecejkP1KK8jZujzHUbwQ

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DS Best of Collection
https://mega.nz/#F!33AhDa4T!awOqr7lhZYFgjXoMMu6_8w

Alt download part 1 https://drive.google.com/drive/folders/15qjCPztI548wV1ocHfYuYWD8vQFgkwJb
Alt download part 2 https://drive.google.com/drive/folders/1oh6ll1ACClxLWIHOEVJ9RBZnD9-xpoxI

DS Cylum's DS Collection, similar to above but with more roms
https://drive.google.com/drive/folders/1w6ydIhY-1GCsPzIIHuVSOYZUNiv67HY0

GameBoy Advance No Intro Password=snahp.it
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https://mega.nz/#!nNoCWbBB!VYNEdwStd12U_aS1qotoo9bz8vky9JnZGrlqAeVKHjA
https://drive.google.com/drive/folders/1pCXaEjukH0NsTsSCb1F0hNbjs8_-LMXf

Gameboy Color Roms No Intro Password=snahp.it
https://mega.nz/#!XUwSBRoD!p3AMxcITVJt0eaJuv1ABucJXdb8fkz6Xt3Y5OJG0_qk
https://drive.google.com/drive/folders/1H4M8ITiPUW7OlLWIgQkxBcXscF0rktJC

GameBoy No Intro Password=snahp.it
https://mega.nz/#!2NgQEaDK!s-pX-87g4s8E6Gw__G6bzyhrxwikPI-_FIStstXhNuI
https://drive.google.com/drive/folders/1JgnLjNZpI0l10GN4OGHr47ceT9yhh4UT
cylum's snes rom set PasteShr cylum's snes rom set

N64 No Intro Password=snahp.it
https://mega.nz/#!TUoBCawT!wtLlUZoozVpk0fAlpF_iZuah2qwVK18JoWQFdKwGjh8
I will find more links for this soon

SNES No Intro Password=snahp.it
https://mega.nz/#!SEA1ARrQ!TLAiO_iBylhvI-8rpK1AAcPfblpQe6anNUoFsz9a6ZY
This is small enough that the whole collection will download under the 5GB cap Mega has.

NES No Intro Password=snahp.it
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https://www116.zippyshare.com/v/FopKXj9d/file.html
https://drive.google.com/drive/folders/1NOAB1iwzxScWxVD-G-a0tKD9BOXHJ4Rr

Game and Watch: collection made by /u/xprism1
https://drive.google.com/drive/folders/1VsRg8wZ2R_r_lRN89dKopQsTVN6EvRU3

Your going to want this program too https://www.7-zip.org/ use 32 or 64 bit depending on your version of OS, which you can check like this,
Windows: https://support.microsoft.com/en-us/help/827218/how-to-determine-whether-a-computer-is-running-a-32-bit-version-or-64
Mac OS: https://www.macobserver.com/tips/how-to/mac-32-bit-64-bit/
I would recommend using a PC to download these files, because a phone while it can open 7zip files, is going to take ages to open some of these folders due to the number of files in them.
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Also if you are download CIA files from 3dscia.com make sure to use this on them to use them with Citra.
https://gbatemp.net/threads/batch-cia-3ds-decryptor-a-simple-batch-file-to-decrypt-cia-3ds.512385/
Then you can convert them to .3ds without issues.
cylum's snes rom set