List of 3DS PC utilities

3DS tmd reader
CTRRPC (RPC server/client for poking the 3DS usermode) by Plutooo https://github.com/plutooo/ctrrpc)
CTRSDK : A set of legal open sources SDK replacement Tools, https://github.com/ctrdev/ctrsdk
EditTMD : (by cearp) https://gbatemp.net/threads/release-edittmd-edit-tmd-files.376426/
p3DS (3DS Python Tool)
NTR Debugger (3DS cFW with wifi debugging tools) (by Cell9)

ROM and Homebrew tools

3DS CTR Decryptor (CTR Keygen+Padgen) [Team VOiD] (move to multi decryptor after page creation) => see: 3DS Multi Decryptor
3DSCRC --> See EvoCRC
3DS Explorer [Elisherer]
3DS Lazy : a ROM editor/rebuilder GUI for different tools Link
3DS Mset Sign (convert launcher dat to GW or HB) [Roxas75]
3DS Multi Decryptor
3DS ROM Converter
3DS ROM Creator [Ernilos]
3DS Key Generator [Team Fail] Link
3DS ROM Editor (by Reisyukaku) https://gbatemp.net/threads/release-3ds_ctr_decryptor-void.370684/page-90#post-5155599
3DS ROM Header Editor
3DS to CIA converter
3DS Tool [Ground](suspiciousware?)
3DS Windows Explorer extension https://gbatemp.net/threads/3ds-windows-explorer-extension.373589/
Card1to2
CCI/CIA Command Builder (aka ROMTool GUI) : (by TiniVi) https://gbatemp.net/threads/tool-makerom-gui.376540/ git
Crappy Tiny Reader CTR
Ctr tool [Neimod] (https://github.com/3dshax/3ds ?)
Ctr tool GUI
CTR Toolkit
CTR Keygen => see: 3DS Multi Decryptor
EvoCRC : Rom Manager and renamer.
exheader injector (by piratesephiroth) https://gbatemp.net/threads/release-exinjector-inject-original-exheaders-into-repacked-roms.373839/
FileXORer (by Xerpi)
Gateway
Gateway 3DS Fragmentation error fixer (by _Tim_) (Gateway 3DS microSD Tool) https://gbatemp.net/threads/gateway-3ds-microsd-tool.369165/
Gateway 3DS Rom Sorter
Gateway ROM Patcher
GatewayFlash (for android)
Gatewayize
GW Decrypt
gw_homebrew
Homebrew Converter (by Snailface)
MakeROM
NCCH_Decryptor
Padgen => see: 3DS Multi Decryptor
padxorer (by xerpi)
PatchROM (riivolution for 3DS) (https://github.com/44670/patchrom)
ROM Tool : manage rename ROMs. Canceled. https://github.com/bkifft/3DSromtool (by bkifft)
ROM Tool GUI : a GUI for ROM Tool on Mac. https://gbatemp.net/threads/release-mac-rom_tool-gui.374640/
RomFSDecryption
RSF Builder : (by TiniVi) https://github.com/TiniVi/RSF-Builder
Sky3DScTool : Edit ROM to CARD2 type and replace ROM header with one from a game in your already filled 10 game list. Forum

NAND - EmuNAND - CFW tools

3NDAN (NAND Analyze)
EmuNAND Tool
CTRcFW (by St4rk)
NAND to redNAND Converter
ctr-nandmount : FUSE tool to mount and browse NAND. https://github.com/yellows8/ctr-nandmount (FUSE = Filesystem in Userspace?)

Network

3DSNUS : (by ground) https://gbatemp.net/threads/3dnus.376488/#post-5219155
3DS Update Checker
ctr-wlanbeacontool : tool for parsing and generating 3DS local-WLAN beacons. by Yellows8 https://github.com/yellows8/ctr-wlanbeacontool
UpdateCDN : Download system update files from Nintendo update server, can be packed in cia for installation on NAND/EmuNAND. Link (by Cearp)
Ninupdates : Scripts to detects Nintendo system updates and generate reports of the updated titles example. by Yellows8 https://github.com/yellows8/ninupdates
MAC Cycle
RelayMyHome : Mac script to cycle MAC for Homepass. https://github.com/taintedzodiac/relaymyhome

Saves and games managers

005tools
3DS Fuse
3DS Game Library [Spayrosam]
3DS Save DeEncrypter
3DS Save Renamer https://github.com/bkifft/3DS_save_renamer
3DSaveTool [Crediar]
CardTwo Save Tool
cart2sav
CTR Savedata (by 3DSGuy) https://github.com/bkifft/CTR_Savedata
DSaveManager [Crediar] http://3dbrew.org/wiki/DSaveManager
PKHex : Pokémon (3DS) SAV/PKX Editor https://github.com/kwsch/PKHeX
R4iSaveMore
Save Manager 3DS

Game and savegame editors

Intelligent Level Editor
Mario Maker 3DS : A Mario Maker 3DS Level editor. https://github.com/Cyrhades/Mario-Maker-3DS
PatchROM (riivolution for 3DS) (https://github.com/44670/patchrom)
Pyramids Level Editor => see: Intelligent Level Editor
Smash Stuff (by Comex)
Fantasy Life Save Viewer/Editor https://gbatemp.net/threads/release-fantasy-life-save-viewer-editor.374495/

Media

3DS Capture Card : http://3dscapture.com/
3DS CWAV ripper [Team Fail]
3DSEncodeGUI : [Spidey_BR] https://gbatemp.net/threads/3dsencodegui-a-multiplatform-gui-encoding-tool-to-the-3ds.315624/
3DS Movie : [Spinal_cord] http://www.socoder.net/index.php?blogs=29000 and https://gbatemp.net/threads/3dsmovie-converter.316170/
3DS VConv : [lmjfemc] https://gbatemp.net/threads/3ds-video-converter.327479/
3DS Video : [SifJar] https://gbatemp.net/threads/3ds-video-beta.315365/
3DS Video Converter: [NekuSoul] https://gbatemp.net/threads/3ds-video-converter.315687/
3DS Video Downloader : [unknown username..., no name in "About" program's menu] didn't find the thread.
3DS Explorer [Elisherer]
MPO Toolbox
3DS online video converter : http://video.online-convert.com/convert-video-for-nintendo-3ds

Others

3DS Controller: Use your 3DS console as Windows controller (sends data to keyboard, joypad and mouse). by YoshiInAVoid Temp. link
3DS Key Bruteforcer
QR BinExtractor (convert a QR picture to bin) https://gbatemp.net/threads/cubic-ninja-qr-code.370922/
RPU : Raspberry Pi Unbricker (Unlock Gateway3DS bricked consoles) https://github.com/bkifft/RPU by bkifft

Pokémon Trainers

KeySAV : Pokémon X/Y Box/Battle Video Data Viewer https://github.com/kwsch/KeySAV2
RSTE : pokemon omega ruby alpha saphir trainer editor https://github.com/kwsch/RSTE
RSWE : Wild Encounter editor for Pokemon Omega Ruby and Alpha Sapphire. https://github.com/kwsch/RSWE

https://github.com/kwsch/xyslot https://github.com/kwsch/xytext Too many tools for pokemon... https://github.com/kwsch