LibreOffice should be higher than OpenOffice, it's much better maintained.
I suggest ENIGMA Game Maker as a alternative to Game Maker. It's libre and Game Maker compatible.
Nano should be higher up than vi/vim since it's easier, and add Links2 to the Linux terminal stuff (it's a text-based web browser that's really good).
Qemu should be on the list of virtualization tools.
Transmission should be first in the list of torrent programs, it's simple, easy to use and has a no-nonsense interface.
Tox should be on the list of chat programs.
DosBox should be added under gaming.
The Darling Project should be there somewhere too.
The Atom editor should be under development tools, and '(IDEs)' should be removed, because there are far more development tools than just IDEs.