Texture Packer-Gui is, as the name states, a GUI for the awesome texture packer that comes with every libgdx distribution.
The application can also be used through command-line, if you need to include texture packing in your build workflow.
Arguments are:
--project="path/to/project/file"
--silent
If you don't want to use project files, you can directly set the input and output directories, as well as defining a settings file.
--input="path/to/input/folder"
--output="path/to/output/folder"
--settings="path/to/settings/file"
The "--silent" option directly packs the given project or input folder without spawning the GUI. Else, the GUI is spawned with input, output and settings set according to what was given.