Various video game related sites

Games to play

A Dark Room
The Mysteries: Mysterious puzzles. Each one offers a few PNGs as a reward for completion.
Habbo Hotel
Skribbl.io
Catfishing: Not a game about catfishing people. I have yet to find anything of that nature. Catfishing is a game about guessing Wikipedia articles by their categories, which is probably more fun anyways.
Flowergame
Xanje
Mweor
Squawk Overflow
Dragon Cave
Wobble Town
Powerpets
Emulator Online
My Abandonware
Old Games Download
Armor Games

Get more from your 3DS

3DS Hacks Guide
Pretendo Network

Wikis and other useful things

Vimm's Lair: Large retro game preservation project (note that even the 3DS is retro now! :'[ ). It's not just games-- this site has manuals, reviews romhacks, and more!
Official Terraria Wiki
Terraria Community Forums
Hollow Knight Wiki: Now with information on both Hollow Knight and Hollow Knight: Socksock.
Pycosites' IV calculator
Smogon: Competitive guides, competitive news, and, of course, Pokemon Showdown.
Global Pokedex Plus
Pokefarm Q: Both of these let you hatch Pokemon eggs with other people online.
Buried Relic: Full of shiny hunting info/guides, mostly focused on gens I-V.
Blue Moon Falls: Very in-depth information on Gens I/II, including why you might like them. To top it all off, the site just looks nice!
Hallowed Tower: All sorts of guides and tools for the mainline Gen IV games. Check out the shiny hunt generator, it gives you a Shiny Pokemon to hunt AND advice on how to hunt it!
Nookipedia
Critterpedia Plus: A very intuitive guide and checklist for the Animal Crossing: New Horizons critterpedia.
Turnip Prophet
Flower Breeding Simulator: Fun way to visualize flower genetics.
Nooknet: Animal Crossing: New Horizons fansite with miscellaneous tools and guides. The main draw is the ability to share custom designs, island tunes, and dreams, but the K.K. Slider album checklist is also quite nice.
Nookazon: Site for trading with other players in New Horizons. You can exchange bells, furniture, island tours, villagers, designs, and more.
Final Fantasy Dawn of Souls official guidebook
WikiBound

Starmen.Net
Earthbound Text Generator