The book featured in the link there is an excellent resource for anyone looking into poisons. It is specifically written to give authors an idea of how different poisons work. It also includes some great information, such as how hard the different poisons are to procure and detect.
Realism vs Fun
There are very few if any games that handle poison in a realistic fashion. There are a couple of basic reasons for that. Poison is a very complicated subject with a huge number of variables. The subject is not handled well by the source fiction. Realistic poison is rarely fun and exciting. So, do we want realistic poison?
In what ways are games typically unrealistic? Speed of onset is a big one, as most fictional toxins act much more quickly than their real-world inspirations. Fictional poisons are also far more lethal, as most true poisons are more likely to make you vulnerable than dead. Finally, games have a history of giving characters ways to simply shrug off any ill effects at all, or to automatically recover as good as new.
But, realistic poisons are often not very friendly to good fiction. That is the primary reason the source fiction handles poison so poorly. In a game, it becomes even more awkward. If you have a lengthy speed of onset, that requires additional tracking. If you want to use realistic poison effects, then you will probably need to incorporate complex rules for modeling them (especially those that impair judgement). Denying PCs a way to avoid the ill effects of the poison is probably going to net you a mutiny, not praise for your adherence to detail.
Thou Shalt Not Suffer a Poisoner
Poison comes with an array of fuzzy and awkward moral questions. Is using poison to kill somehow less ethical than using a blade or bullet? Does the answer change depending on whether a PC is the poisoned or the poisoner? We can certainly see that it varies from genre to genre. And yet, I think I could name a hero in just about every genre that would use poison of one stripe or another.
I certainly tend to think that poisoning is unheroic, and frequent use will reshape a campaign. On the other hand, the party line of early editions of D&D that using poison is an evil act is too far for me. Also, it gets far more difficult when you start looking at fiction, as poison often ends up being a way for the hero to turn the tide against a stronger foe. Don't believe me? How did Harry Potter destroy the horcruxes? Yup, that was basilisk poison. In a number of genres, some sort of sleeping poison acts as a way to humanely overcome the mooks without the hero having to sully his hands with bloody violence (q.v., Green Hornet).
I think that if we could find a way to model poisons in the system in a way that is fair, reasonably realistic, and not terribly complicated, the ethical questions could be reasonably easily set aside. Admittedly, this may be a terribly naive and optimistic thought. I would like, though, to see an archer that dips his arrows in a paralytic, or a superhero gadgeteer who uses a gas gun, or a ninja who silently takes out the guards with a blowgun. Those seem like eminently reasonable character concepts to me.
Boiling It Down
So, how should we model poison in a system? Well, obviously, it depends heavily on the base system. There are a few general guidelines, though. First, you probably want some way to easily extend your rules to cover the massive variety of possible poisons without becoming massively complicated. This is one area where the d20 system does fairly well. By overlapping ability score damage with conditions, you can end up with a pretty remarkable variety of effects that can be expressed very simply. A system like World of Darkness, in which the poison simply reduces your available dice pool, is very effective at modeling the general penalties of poison, but doesn't allow for much variety in effect.
Onset time is definitely an issue. If you have something on the order of 6-second combat rounds, most realistic poison is simply not going to take full effect before the combat is over. While it can be nifty to have the PCs worry about the lingering effects of poison from a foe, it does make poison use on the part of the PCs tricky. After all, in most campaigns, the PCs don't allow their foes to run away, so lingering effects are rarely interesting from a story perspective, or effective from a tactical perspective.
It makes a lot of sense for poison to have progressive effects, rather than a simple "you are poisoned, take -2 to all actions until cured." Much like with the possible effects, though, you have to be very careful to avoid making this too complicated. Unless you are running some kind of game where poison is common (such as an espionage game), the rule will probably only come up once every five or six sessions. Unless you can express it very simply, and make it easy to track, it probably isn't worth the effort. Systems with condition tracks are likely to be very good at this. Systems with very abstract timing (e.g., round, scene, session) are likely to be very bad at this.
Should poison have very long-term or even permanent effects? Well, aside from those that are fatal, obviously. I'm actually going to vote against realism here. Long-term damage just sucks. It is pretty rare that it actually adds anything to the experience of play. I don't think that any poison should have an effect that lasts beyond the end of the current story.
What's Your Poison?
How do you handle poison in your campaigns? Do you have any favorite rules for it? Do you think it's evil?
I've seen a couple of sourcebooks that were all about poison, and there were a couple of good articles on it in Dragon Magazine. But, ultimately, I've never found a system that manages to be elegant enough to be easily remembered and used, effective enough to be a viable option, and evocative enough to feel truly toxic. If any of you out there have any good suggestions, I'd love to hear them.