The Everdrive Packs (by smokemonster) This pack focuses on sorting and being ready to use (with flashcards, but obviously works with emulators). It includes only 1 version of every game, the US version being preferred, with the addition of exclusives from other regions. However it also includes zipped region add-on packs that add back all roms of that region. This pack in addition to the official roms also includes notable romhacks, translations and homebrew in their own folders. More info about the pack:

https://www.epforums.org/showthread.php?101715-EverDrive-Packs-Release-Thread

This is a full collection as of 9-5-2018, inclusive of GB, GBC, GBA, N64, NES, SNES, and others not necessarily limited to Nintendo