So I argued pretty strenuously against the excuses used to keep PCs from using poisons freely in a campaign.
But what if you want to allow poisons, but not make it free use for any and all, in all circumstances?
What are some limitations that won't break kayfabe, and reveal you're doing it just to avoid the headache of all those resistance rolls and arguments about poison coming off on a parry or why it doesn't wipe off your blade when you stab through cloth armor.
Speed of effect. Poisons aren't generally that fast. If you die in an hour from a real-world venom, it's a pretty potent one. Limiting immediate-effect poisons by increasing their cost (since they're riskier to gather, riskier to handle, and more potent) is fair. Save-or-die-instantly poisons should be costly and rare. The longer it takes to work on someone, the less costly it should be assuming it's a poison intended for combat.
Scope of effect. The more common, cheaper poisons should be less effective. Every game I know does this. But it's common to address poison as if it's the save-or-die level stuff. Make lesser versions available, make non-damage causing or even non-lethal (but not necessarily safe) forms available. A poison that causes shaking and twitching for an hour or so or causes excruciating pain for a short time might be handy, although again the cost will vary depending on the speed of effect and scope of effect.
Size of dose. Simply put, big monsters should need more poison to kill. A man-killing dose of cobra venom or grue snot might not be enough to really bother a 1,200 lb. owlbear, nevermind phase a multi-ton dragon. Too small of a dose should give improve resistance and/or reduced effect.
Combining the three above will help limit usage in fights to an extent - poison won't really help you take down your enemies more quickly. It's really there to ensure they die from a hit, not to ensure they die from a hit right now.
Some other things to consider:
Weapon limitations Some weapons just won't be able to carry much of an effective dose of a poison. Crushing weapons that lack penetrating spikes will need a contact venom and skin contact. It's not likely to work that quickly, either. Swords and other large weapons may require multiple doses (they do in GURPS, although DF handwaves that away), and might not "hold" poisons very well. Gummier/stickier substances might exist, but then you have the issue of cleaning them off of your weapon. Weapons may suffer from repeated use in this fashion - earlier rusting or pitting, longer cleaning times post-fight, issues with incomplete cleanings. Otherwise you might have to take your chances - wipe the blade with the giant scorpion venom just prior to combat, and wipe it off after, and hope you get some of it into the target during the fray.
Disposable missiles won't have so many of these issues - blowpipe darts might easily be poisoned and then just chucked out if you don't use them in a timely fashion. Arrows and quarrels with breakable poison vials behind the head don't need to be recovered (although you may want to lop off any distinguishing feathering, if you don't like letting people know who shot those arrows). I'm not sure it's feasible to hollow out a sling bullet in such a way it will still be hurl-able but also release venom ounce it penetrates. Thrown weapons suffer some of the same limitations as melee weapons.
So a potentially reasonable limitation is to make it harder, or more consequential to the user, to envenom some weapons.
Market Availability. Make them roll to see if there is any for sale. Pretty simple. It won't always be available. It won't always be plentiful, especially if it's very effective (someone will already want to use it).
License Required. You might need a specific license to use poisons, or carry them. It might be expensive, socially limited, or needlessly complicated to get one. It might expire and need renewal. You might need to explain to the local lord why you need 25 doses of Bladeblack and why he shouldn't be worried about you.
Limit antidotes. It's not like the apothecary has the specific antivenin you need at all times in all amounts. And a wise one will charge a lot for them, since you're likely to pay the gold instead of risking lingering death.
Acceptable Targets. Make it socially unacceptable to use poison against certain opponents. Pretty simple - and usually that'll mean other "people," however that gets defined. Provide appropriate social opprobrium for using it on the wrong target. "Black Mark isn't using his poisoned arrows just on orcs, you know. They say he shot down men with it too . . . "
Still, it's likely such ill-fame won't apply if you're restricting your use to clearly inhuman and unpleasant targets.
Limit the effective targets. No everything is vulnerable to poison; some might require a specific one to deal with. Perhaps werewolves can be slain with a suspension of powdered silver but not by any other normal venom. Maybe orcs are flat-out immune to most of available stuff. ("Grok hate arsenic! It too acidic on Grok's tongue. Grok like taste of cyanide.") Perhaps the issue with monster-hunting with poison isn't moral or practical, but rather just useless - they aren't bothered by the stuff. Resistant to Poison (+3) is only 5 points, (+8) 7 points, and immunity is 15 points, and they might get sprayed around a lot. Poison might be only a special-case issue, or you might need to find the specific bane for that species or just not bother.
Those are just some limitations I think are defensible, if you make them plain from the start of the campaign (or when they enter a new area). It's more the "no, and here are some over-the-top and vague reasons why you can't" reasons I find fail to convince me. You don't need to use all of them, but even a few can prevent poisons from becoming too useful of a tool, and keep them in their place and valuable edges but not the whole of your campaign's anti-monster efforts.
Oh, and obviously, monsters use poison right back. The goblinoids in my game world do, for instance, and every poison needle trap in the world must have been set by someone . . .
Editing later: Talysman posted a nice article about poisons on his blog. I posted some more ideas in the comments.