Greenshot runs in the system tray and registers global hotkeys (Print Screen by default). Hotkey bindings are stored in HKCU\Software\Greenshot.
All settings are duplicated in %APPDATA%\Greenshot\greenshot.ini — the INI file is the authoritative source; registry settings sync from it.
The startup run entry (HKCU\...\Run\Greenshot) is added by default during install; deselect "Start Greenshot at Windows startup" in Settings to remove it.
Greenshot supports plugins (Jira, Confluence, Imgur uploaders) which may add subkeys under HKCU\Software\Greenshot\Plugins.