There are so many apps that its hard to know how to use them all. This guide lists the usages of the most popular ones, but might grow further in the future.
► The Homebrew Channel -- Of course you need to know how to run your homebrew
► Bootmii -- Creating a NAND backup is always a good idea
► AnyTitleDeleter -- As the name suggests, this can delete any title (channel, IOS, ...) of your Wii.
► CrazyIntro -- Replace your Health screen and assign custom shortcuts to apps
► DOP-Mii -- Update your IOS's, system menu, shopping channel and more!
► Emulators -- Various emulators for the Wii
► FTPii -- Manage you SD card on your pc, without taking it out of your Wii!
► HideAndSeek -- Hide your channels from view. Only crazyIntro can launch them!
► Homebrew Browser -- Download many homebrew apps with the Nintendo WiFi connection
► Loadmii -- A homebrew loader that can load form SD and USB
► Mighty Channels -- Loads Virtual Console and WiiWare games from an SD card or USB device.
► NandClean -- Remove all invisible marks of your NAND.
► Reggie! -- New Super Mario Bros Wii level editor.
► Savegame Manager -- Manage your savefiles, on the homebrew way.
► Simple FS Dumper -- Dump your NAND for SNEEK, Triiforce and more!
► SNEEK -- Never use your real NAND again!
► Triiforce -- A VC/WW launcher that uses NAND emulation to load from SD or USB.
► Wad manager -- Install new channels, IOS and more!
► Wiiload -- Send files to your Wii over Wifi