The Command System is the computer/software run by a Zoid's main computer. This is used as a sort of BIOS for the Zoid's computer that provides target information, Zoid system states, communication, etc. This is mostly mentioned in Zoids: New Century, where pilots receive Command System Freezes when their computers have frozen or been overloaded on information after attacks, thus rendering their Zoids inoperable. These errors are not permanent, as the Zoid can be brought back up and running again after the system has been rebooted (the information shown on a Command System Freeze is similar to that of a regular PC's blue error screen, where errors or routines have been overloaded or frozen during execution of the Zoid's main combat computer). It is unknown whether the Command System is already programmed into the Zoid or if it must be separately installed after the Zoid's manufacture, as in episode 7 of New Century, Leena bought a new Gun Sniper to replace her totaled Dibison, after which Jamie and the mechanic at the shop where Leena had ordered her custom Zoid reminded her to install the system, thus implying that a Zoid must be programmed with a Command System before operation.
In Chaotic Century, Command System Freezes are also shown, although they play a relatively minor role in the plot. In several events in the show, there is a distinction between a Command System Freeze and a Combat System Freeze. A notable example of this is in Chaotic Century episode 18 where the "Combat System" of many Zoids inside Mt. Osa encounter a freeze. Unlike the Command System Freeze, which would render Zoids unable to even move, the Combat System Freeze only prevented the Zoids from fighting and/or using its weapons, allowing Zoids to continue moving.
Another example of a Zoid needing computer systems to operate its weapons is in Zoids: Guardian Force Episode 11, where the Storm Sworder Stealth-Type was not outfitted with its Command Options, meaning that when it undertook bombing runs, it was forced to use Redler munitions (though it was still able to use its blades).