Rats are known to tread water for up to 48 hours before eventually succumbing to exhaustion and drowning. And drowning in itself is an agonizing death. We have evidence of that from people who've nearly died of drowning and have been revived.
I don't think putting them in a box with a snap trap would be a good idea. They'd be running around frantically, and could run over the trap wrong and wind up horribly injured but not dying.
Blunt injury can be a humane way to kill an animal, but you have to be able to destroy the brain instantly for it to be clean. I've killed fatally injured lizards (from cat attacks) by placing them on a sidewalk, covering them in a paper towel to keep them calm, and using a brick on the head, but it has to be one swift, clean, confident motion, and I wouldn't be confident that it could be done properly with something the size and wiggliness of a rat.
Cervical dislocation is a humane way to kill rodents when done properly, but is mostly used by people raising domestic rodents as animal food, and would probably be difficult to do with a wild rat.
Carbon monoxide can theoretically be used, but requires some precautions to be humane, and also to be safe for the humans involved. Carbon monoxide technically kills by suffocation, by replacing the oxygen in the blood with carbon monoxide. However, the body measures need to breathe by amount of carbon dioxide in the blood, rather than amount of oxygen. Carbon dioxide overdose causes panic and a feeling of suffocation, carbon monoxide doesn't. That's what makes car exhaust trapped in an enclosed area so deadly- a person in carbon monoxide will feel tired, then eventually pass out, without ever knowing anything is wrong. We've also had people revived from almost dying of /that/, and as such have first-hand accounts of it not being particularly unpleasant. The trick is figuring out how to do it without just flooding the rodents in car exhaust contamination and heat that burns their lungs. Not the best method in many cases, but an improvement over drowning if done right.
And then, of course, the best way to deal with rodents is to not have things that rodents want. You can kill all the rats you can trap, and if they're still being brought in, you'll never be rid of them. That means putting food in containers they can't get into, putting edible plants up out of reach, blocking up whatever holes they're using to get in, and otherwise making the area as inhospitable as possible for them. For outdoor areas, attracting nonvenomous snakes can also be useful- aside from directly eating the rodents, their smell will scare rodents away. Plus, you get to see neat snakes. Another bit of natural control is to put up an owl house. If you get lucky and have owls nest there, they'll catch hundreds of rodents a season to feed their babies.
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