Well, ironically, the biggest use for pokémon poison (or venom) is … in medicine.
Hold on. I don’t mean that kind of medicine. I mean pokémon venom can be used to synthesize medications meant to treat a wide variety of diseases. For example, ekans venom has a variety of medicinal uses, including as a cancer treatment (as it can be used to attack cancer cells), a treatment for parasitic conditions (as, again, it can attack parasites found in the blood, most notably the ones that cause malaria), a treatment for high blood pressure, an anticoagulant, and even as a painkiller. Likewise, there are a few experimental medications for neurological disorders (particularly epilepsy) that have been synthesized from ekans venom, purely because, well, ekans venom is a powerful neurotoxin. (Currently, most medications for neurological disorders are synthesized from either gastly gas or Poison Powder, if they’re not wholly chemical in nature, but there’s research out there that suggests ekans venom would be more potent. Arbok venom even more so, but … baby steps, as they say.)
And of course, outside of ekans venom or the above-mentioned medications, venom is often used to create antivenom. Most hospitals will carry stock antivenom for each possible species of poison pokémon; this is because each specific antivenom is custom-created from antibodies harvested from certain lab pokémon and rabbits. (It sounds barbaric, but it’s actually done in a perfectly ethical manner … and also, it’s pretty much the only way this can be done without being inhumane to people.) For those curious, trainer-grade antidote (that is, the stuff sold in pokémarts) is actually synthesized from standard muk venom, as this is the most potent available.
Outside of the medical industry, some poisons—particularly those derived from acid-based attacks (such as, well, Acid)—is sometimes incorporated into potent cleaning supplies, as such substances are capable of eating through rust, calcified build-up, and other forms of age and decay that are extremely difficult to remove with soap and a bit of effort. In its purest form, this acid may also be used in manufacturing as a means of cleaning and sterilizing not only equipment but also products in production as well.
In short, pokémon venom is primarily used for medicinal purposes and secondarily as industrial cleaning solutions. That’s just about it, really.
Legally speaking, anyway.