Like the DS, the 3DS has a pretty active homebrew community. Even still after the release of the Switch. There's a compelling argument to make that with homebrew, the New 3DS is the ultimate portable game platform.
Make sure to check the DS Homebrew article for more.
A note: some of the more intensive stuff performs worse on the Old 3DS and 2DS. The New 3DS and New 2DS performs better with pretty much everything.
|Half Life (Xash3DS)||FPS||Yes, Half Life on the freakin' 3DS! Some crazy Russians managed to reverse engineer GoldSource and made it open source (Xash 3D). This port is based on that. Runs a bid sluggish on O3DS, but performs better on the N3DS.|
|Quake 1||FPS||Pretty great port. Even includes online multiplayer!|
|Quake 2||FPS||Pretty basic port. Runs in software mode, but performs decently.|
|Quake 3 Arena||FPS||Pretty good port. Somewhat sluggish on O3DS.|
|Doom (PrBoom)||FPS||Includes Music playback that the DS port lacks.|
|Wolfenstein 3D||FPS||Pretty basic port.|
|Duke Nukem 3D (EDuke3D)]||FPS||Hail to the King baby! Runs pretty well. Sadly, Ion Fury isn't compatible but could be if someone bothers to update the port.|
|Lemmings||Puzzle||It's Lemmings on the 3DS. Yep.|
|Retroarch||2nd-4th Gen systems, PS1, et.al||Offical port by the libretro team. The basic cores (2048, NES) run full speed on O3DS, while everything else is near full speed. N3DS has better performance. Even PS1 emulation works extremely well on there (2d games, early 3d stuff). O3DS users might want to check on the other emulators below for better performance. N3DS users might want to stick with this for all your emulation needs.|
|mGBA||Game Boy family (GB/GBC/GBA)||Official port, developed along side the other versions. Runs pretty well. Also great for GB/GBC games as well. Supports the gyroscope for games that use it (WarioWare Twisted, Kirby Tilt N Tumble).|
|SNES9x||Super Nintendo||Most games run full speed on O3DS. SA-1 and Super FX chip games have performance issues. But on the N3DS, everything runs full speed. There's also BlargSNES if you're having issues with SNES9x.|
|VirtuaNES||NES / Famicom||Good emulator, but not super accurate. Retroarch has Nestopia UE core if accuracy matters to you.|
|PicoDrive||Mega Drive / Mega CD / Master System / Game Gear||Pretty good Sega 8/16-bit emulator. No 32x support like the Retoarch core.|
|TWiLightMenu++||Menu Replacement||An open source replacement for the DSi Menu. Can be used to launch DS and DSi games from your SD card slot. No Flashcart required. Also includes some neat features like cpu speed up for DS games.|