The first charting program (in no particular order) in the main three that people use. This charting program was made with Clone Hero in mind, and features a lot of nifty bells and whistles. Those include (but are not limited to): export song.ini, solo section cues, playable in the charter mode, keys and mouse placement modes, extended sustains, and even drag and drop functionality.
The second charting program that is part of the main three that people use now. Is mostly used by people who come from the Frets on Fire forums side of charters.
As explained on the GitHub: "EOF is a song editor for Frets On Fire, Phase Shift, Rock Band and Rocksmith. The aim of EOF is to provide a simple process with which to create songs. Just provide an OGG file and spend a little time designing note charts and EOF will save files in the appropriate format for immediate use with Frets on Fire and Phase Shift."
The last charting program that is part of the main three. This charting program is used mostly by people in the Custom Creators, or C3, community. It is used by Harmonix and is more than just a charting program, as it also is a full blown DAW (Digital Audio Workstation). It is a "free trial"(That never ends like WinRar) but you get full access to the product with the free trial. The technical full product costs at least 60$ US if you feel like supporting them and not seeing a "this is a free trial" screen every time you open it.
From Reaper's home page: "REAPER is a complete digital audio production application for Windows and OS X, offering a full multitrack audio and MIDI recording, editing, processing, mixing and mastering toolset."
The most used charting program back in the initial craze of custom songs. There is a new, currently being worked on new version of Feedback you can find here, but this is going to be focused on Legacy Feedback, as I, (ZeroHearts) know nothing about the new one.
It is highly recommended not to start with Feedback if you are just getting into charting, as it is an old program that doesn't have nearly as much usability as any of the other ones. (Plus it looks straight out of Windows 95, so that's a thing). It is a fantastic and beautiful relic of the past, but maybe it should stay that way.
From the GitHub: "Here lies the original 'FeedBack' Guitar Hero custom song editor that spawned a craze of custom cong creation for the popular Guitar Hero and Rock Band games.
I have since started a new 'FeedBack' project which will implement all of my ideas from the time I started the project back in GH1 days. It will feature a full game mode, and support for many more instruments. This remains here for nostalgia, or future hackers interested in tweaking the original tool."