As of this opening post, the 3DS and WiiU eShops will be closing in 9 days. It's best to grab any digital console exclusives that you can before they're gone for good. Here's some recommendations from me:

WiiU:

Affordable Space Adventures

NES Remix 1 & 2

Dr. Luigi

Mario vs. Donkey Kong: Tipping Stars

Mini Mario & Friends: Amiibo Challenge

Pushmo World

3DS:

Attack of the Friday Monsters

Photos with Mario

Pokemon Dream Radar

Cave Story

Poke Transporter

Pokemon Bank

Pushmo

Stretchmo

Crashmo

Shovel Knight (has 3D function)

Pokedex 3D Pro

Fun! Fun! Minigolf Touch!

Soccer Up 3D

Azure Striker Gunvolt

Zombie Panic in Wonderland

Kirby Fighters Deluxe

Swapnote

Flipnote Studio 3D

Retro City Rampage

Ikachan

Swapdoodle

Team Kirby Clash Deluxe

Gurumin 3D

The Denpamen: They Came By Wave

Liberation Maiden

Kirby's Blowout Blast

Dillon's Rolling Western

Rusty's Real Deal Baseball

Colors! 3D

Sakura Samurai: Art of the Sword

Pokemon Picross

Shakedown Hawaii

DSi Games:

Shantae: Risky's Revenge

Zelda: Four Swords Adventures Anniversary Edition

Anonymous Notes 1/4

As for Virtual Console releases, here are some titles I recommend that can be found on the 3DS, but some are mostly 3DS releases. I recommend these as Nintendo may or may not rerelease them for their Switch Online service

The Legend of Zelda: Oracle of Seasons/Ages

Tails Adventure

Legend of the River King

Milon's Secret Castle

Shantae

River City Ransom

3D Classics: Kid Icarus

Kirby's Dream Land 1/2

Super Mario Land 1/2

Kid Icarus II: Of Myths and Monsters

Alleyway

3D Shinobi III: Return of the Ninja Master

The Legend of Zelda: Link's Awakening DX

Mario Golf/Mario Tennis

Metroid/Metroid II: Return of Samus

Super Mario Land 3: Wario Land

Wario Land 2/3

Donkey Kong Land 1,2 and 3

Super Mario Bros. Deluxe

Game & Watch Gallery 1,2 and 3

3D Gunstar Heroes

Defenders of Oasis

The Legend of Zelda and The Legend of Zelda II

Pokémon Red/Blue/Yellow/Silver/Gold/Crystal

Mega Man Xtreme 1/2

Mario's Picross

Kirby's Block Ball

3D Classics: Kirby's Adventure

3D Classics: Excitebike

3D Sonic the Hedgehog 1/2

The Mysterious Murasame Castle

Kirby's Pinball Land

Gargoyle's Quest 1/2

Donkey Kong for Game Boy

3D Streets of Rage 1/2

3D Altered Beast

Sonic the Hedgehog 1/2 for Sega Game Gear

Sonic the Hedgehog in Triple Trouble

Super Mario Bros. 1,2 and 3

Balloon Fight

Balloon Kid

Vampire: Master of Darkness

Castlevania 1,2, and 3

Crash 'n the Boys Street Challenge

I honestly believe that whatever title you want, the future will provide purchasing options for you. The real crush is what price are you willing to pay? Nintendo will be making new game buying venues going forward - that is the business they're married to. But we all know the asking prices will be higher, so for this round . . . the clock is ticking!

I liked how the 3DS eShop was home to some known and obscure Sega Game Gear titles, one of my first must buys for the system was Tails Adventure, which served as a prequel story, before Tails met Sonic and it was basically like Metroid, finding new gadgets to use and backtracking to certain areas in a location that you couldn't get past before, highly recommended!

As of now, the Wii U and 3DS eShops can still be accessible, however all of what was on the main page along with purchasable games have been completely wiped clean, leaving a big white void of nothing but your account profile. Here I decided to show the last few minutes of what the Wii U eShop looked like before the changes were made. Enjoy its last moments here!

Kinda feels like they killed the last bit of Satoru Iwata's legacy. I'm not a fan of the direction Nintendo is going without him. The Switch is popular, but I gotta say it feels flimsy compared to the WiiU and a subscription instead of the Virtual Console just has no value to me. 

I think the saddest losses are the games that'll probably never be playable on another system, like Lost Winds 1 & 2 from the original WiiWare. That was shut down long ago but can still be played on WiiU if you already owned it. Games like that are going to be totally lost to time. 

@MamboGator

Not lost if you think about emulators

@Benjanime, true. I haven't had much success emulating any disc-based consoles though. I got some Sega CD games working on my AtGames arcade cabinet, but even trying to mod a PS1 mini to run retroarch ended up not working. The games worked for a while but then it stopped booting from the USB and defaulted back to the preinstalled games for some reason.

Compared to cartridge ROMs, it's a lot harder. For me at least, but I'm certainly not the smartest cookie in the shed.