Although the warring countries at The End used many different kinds of weapons, only two have been described in the story so far.
A form of radiation harnessed by the inventor Sam (Sparkplug) Sanders for Apex Industries. Amesworth radiation is used in ray guns and disintegration beamers. As mentioned in the comic, if the radiation is strong enough it will disintegrate anything. At lower levels it only affects organic matter. (Twinkies are thus identified as inorganic). It is named after its discoverer - Dr. Eden Amesworth, who Sanders may have actually met at one time.
The Mutagenic VirusEdit
This has not been explained in any detail so far and may not actually be a virus. This is the thing that turns humans into mutants, and is present throughout the planet. Generally it is referred as "the mutagens". It's questionable as to whether the mutagens were initially intended as a weapon, or if it was accidentally leaked from somewhere.