Hello all! I've found that after modding my 3ds using this guide: https://3ds.hacks.guide/
It was so easy, that figuring out how to do anything else was a pain, and there were no concrete step by steps like this one for what I wanted to do! So I want to just quick share with you some easy tutorials for how to get more out of your modded 3ds in one big masterpost here!
Downloading 3ds/Virtual Console Games:
All 3ds and Virtual Console games can be found in easy qr code forms here: Home Page | hShop (erista.me)
To download them, just open the FBI icon on your 3ds (it should be there after following the guide above!) and go down to "Remote Install" then click on "Scan QR Code" and use the camera to scan the games onto your 3ds!
Downloading DS Games/Getting them on the home screen:
Downloading DS games is a bit trickier, but once you know what to do it'll become second nature!
First, you need to download two new homebrewing software off of the "Universal Updater" app (which should be on your 3ds already!) You're gonna download "TWiLight Menu++" (Which allows your 3ds to run DS games) and "ndsForwarder" (This is what's gonna put your games on the home screen!)
Next, search for the games you want on this website: Vimm's Lair: The Vault It has tons of preserved games you can download!
Then, take out your SD card and put it into your computer, simply transfer the .nds files you downloaded into the following folder: "roms" -> "nds"
(The "nds" folder may have a note in it saying "place nds files here!")
The game will be downloaded onto Twilight Menu then and you can stop there, but there's one more step to take if you want your games on the home screen! Open up "the homebrew launcher" on your 3ds and scroll down to "NDS Forwarder Generator" you're then gonna see a copy of your SD card's folders, so open up "roms" -> "nds" again and there are all your .nds files! Just click on them to install them onto the home screen, and done!
Downloading Gameboy Games:
Downloading Gameboy games can work the same way as above, but there are some cons to that method!
First, go to "Universal Updater" to download "GBARunner2" (so that your system can emulate Gameboy games!)
You can then use the same method for DS games for Gameboy games, however, they will only be accessible through Twilight Menu, and won't have icons! If you're ok with that, stop here!
If you want Gameboy games on your system's home screen with icons, continue!
You're gonna need to download an application on your computer called "New Super Ultimate Injector for 3DS" The download link can be found here: [DISCUSSION] New Super Ultimate Injector (NSUI) | GBAtemp.net - The Independent Video Game Community
Next, find your desired game off of Vimm's Lair: The Vault and open up the file in the appropriate category in the injector (Open .gba files in the Gameboy Advance Category) Go to "File" -> "New" -> "Your desired game CIA"
Here, you can change the title of the game, the icon that appears on the bottom screen, and the bigger virtual console icon that appears when it's hovered over! Vimms has some graphics you can use in the vault, but you can also find some yourself to get the ones you want specifically!
Go to "Project" -> "Load ROM" and choose the file you downloaded from Vimm's Lair.
The information for the game should automatically fill out, except for the graphics. Click on "Load Image From File" on the left side to upload your choosen icon. Click "Load Image From File" on the right to upload the larger graphic.
After that's done, go to "Project" -> "Export CIA" to download your new .cia file of the game! Then, pop your SD card into your computer and drop your new file into it. (it does not need to go in a specific folder, just the root of the SD card!)
Finally, go to your "FBI" icon and click on "SD" then, just scroll down to your .cia file and install it!
I believe this method could also be used to emulate many other types of console games, however, I have not tried yet, so I'm unaware on what homebrew apps to use.
Custom Themes:
Custom themes can be found here: Themes | hShop (erista.me) or here: Themes | Theme Plaza Simply use the same qr code scanning method used to download 3ds games above!
Then, open up "Anemone 3ds Theme Manager" on your 3ds to install them onto your system! If the theme has a checkmark next to it, that's how you know it's active!
That's everything that I've discovered for myself so far! I hope I'm able to help at least one person in their modding journey! Let me know if there's any questions, and I can try my best to answer them! I'd also love if you shared some discoverys you've made yourself!