Biological Warfare (Apocalypse)
Biological Warfare can be considered the ultimate human-designed weapon to fight the aliens. Either this or the Devastator Cannon can be considered your "standard issue" alien-slaying weapon in the mid-to-late game.
The Toxigun is one of the most powerful weapons in the game, available upon the completion of Biological Warfare research. Not only do the toxins specifically target alien biologies, but Toxigun shots can pass through Personal Disruptor Shields without destroying them. Note, however, that the toxins do comparable damage to the M4000 to human adversaries.
"An X-COM weapon designed to shoot high powered projectiles containing anti-Alien toxic fluids. It is designed to cause minimal harm to other targets and is not very good at penetrating armor."
With the Toxigun comes Toxin A. While it is weak, it does have the ability to bypass (and thus capture) shields. Nevertheless, Toxin B is usually available right after researching Toxin A and is much more potent.
"Ammunition for Toxigun. It contains a lethal fast acting poison designed to target Alien life forms. It is not so effective against the more advanced bipedal Alien types."
Toxin B is a step up from Toxin A, but still not as potent as Toxin C. Takes 1-2 shots to kill Skeletoids or Anthropods.
"Ammunition for Toxigun. It contains a lethal fast acting poison designed to target Alien lifeforms. It effectively renders the earlier A-type toxin obsolete because it is more powerful and more effective against the higher Alien life forms."
Toxin C. This is the pinnacle of anti-alien warfare. A couple of shots will render even the hardiest Megaspawn dead at your feet. A great weapon, to be sure, but still lacks the ability to recharge. I use Devastator Cannons more often than this, but it is a good weapon nonetheless. NEVER use this weapon if you cannot mass-manufacture Toxin C. Otherwise your troops will end up without ammunition, which tends to put a damper on your success in battles.
"Ammunition for Toxigun. A fast acting poison which targets all Alien life forms with equally devastating effects. This toxin effectively supersedes the A or B types."