UniversalUpdater This is like a package manager for HB Apps that also provides an easy way to update them.

Checkpoint/JKSM Save manager for games. Always good to backup save data or to extract them for editing.

TWL Patcher Featured in my last post, DS game upscale and widescreen patches.

Pretendo/Nimbus Custom online play server from the pretendo community.

Anemone3DS Theming tool for 3DS HomeMenu. With direct download support and QR code scanner. Very convenient

Fast PlayCoin Set your playcoin count to 300 instantly. Also possible with JKSM

FBI Title Manager and installer, also with QR code and URL support.

ftpd pro FTP provider for 3DS, my go to tool to transfer files.

GYTB Custom HomeMenu Badges

ModMoon Mod manager for 3DS.