Some homebrew I recommend are:
FBI: https://github.com/Steveice10/FBI (Homebrew Installer)
Universal Updater: https://universal-team.net/projects/universal-updater (repository for installing other homebrew. Note that most of the other homebrew listed can be downloaded and installed using this)
Anemone3DS: https://github.com/astronautlevel2/Anemone3DS/releases/tag/v2.3.1 (Custom Theme homebrew)
snes9x_3ds: https://github.com/bubble2k16/snes9x_3ds/releases (snes emulator compatible with both old and new 2/3ds models and that boasts quite good compatibility.)
HShop: https://hshop.erista.me/ (The go to source for 3ds games)
TwilightMenu++: https://github.com/DS-Homebrew/TWiLightMenu/releases (Allows launching DS roms from an SD card)
Some useful sites and tools you may want to check out:
NSUI: https://www.gamebrew.org/wiki/New_Super_Ultimate_Injector_3DS (Fantastic piece of software that lets you encapulate roms as .cia files allowing them to be installed to the 3DS home screen, must have imo)
ThemePlaza: https://themeplaza.art/themes (site that allows you to scan and download custom themes through Anemone. Using the website with QR codes is greatly preferable over the built in theme browser in Anemone as it is slow)
The Emulation Wiki: https://emulation.gametechwiki.com/index.php/Main_Page (This is a great general source for emulation information, but also has great resources for emulation on the 3DS. It's a very useful site imo)
CD Romance: https://cdromance.com/ (This has quickly become one of my favorite rom sites as it has a great selection of translated games and DS roms in general. Hshop is still preferable for 3DS games however.)
Vimm's Lair: https://vimm.net/?p=vault (The tried, the true. Vimm's Lair is a good source for clean rips of official roms. Their gamecube isos are nkit.iso but that hardly matters for the subject at hand. Imo, they are the best option for GBA games.
If anyone has any questions feel free to reach out.