What I like about this thread (aside from the sex and sheer awesome of most of you) is that it causes me to rethink some of the things I've always written.
For example, when a trainer dies, I don't really assume that the Pokemon dies with them. (Mostly because I really can't explain how that would be possible, considering the fact that it's never mentioned that the trainer's life force is tied with his Pokemon's. I suppose it's implied by the first movie, but then again, Ash was revived by Pokemon that weren't his as well.) Instead, I assume that the Pokemon are simply transferred to a living relative (if any) or kept in their Poke Balls until someone comes along to release them and destroy the Poke Ball.
Mostly, I get the latter idea from the episode "Just Waiting On a Friend," the one where the Ninetales is left alone at a mansion long after her master died. She's still alive and well; it's just that the Poke Ball is keeping her where her master lived. On the other hand, it's also a very old Poke Ball that's keeping her there, so it could be that things are different with newer versions.
For that reason, I also tend to think of the Poke Ball as the one thing that marks a Pokemon's capture. As soon as a Pokemon is captured, the ball "writes" the Pokemon's data within itself. So, the ball needs to be damaged, destroyed, or wiped before a Pokemon can really be freed. Additionally, it's possible for more than one Poke Ball to attach itself to a Pokemon (See Red's capture of Misty's Gyarados in Special.), but in most cases, the Pokemon will break free out of loyalty to its previous owner. (I tend to use the fact that Charmander looked pissed when Ash nearly caught it in "Charmander - the Stray Pokemon." The ball could have worked, but Charmander broke free from the ball because of its strong desire to be back with Damian.) The only other thing stopping the capture of a Pokemon already owned by a trainer is that it's just incredibly taboo to do so. That and the likelihood of a Pokemon breaking free from its ball (and therefore damage a ball in the meantime) renders the attempt to do so incredibly expensive. Snag Balls, meanwhile, tend to be "powered up" by the Snag Machine, so it's slightly more potent and more likely to override a Pokemon's loyalty to its owner.
With the question of what state a Pokemon is in while they're inside a Poke Ball, I consider them to be in something like suspended animation, where a Pokemon is simply kept at the exact same state they were in before they entered the ball. So, a Pokemon will never get hungry if they weren't before they were recalled, but if they were poisoned, the poisoning will still run its course until the Pokemon inside the ball reaches a critical point. Meanwhile, mental ailments like weariness and confusion will probably wear off because the Pokemon is, in a sense, taking a rest.
Or, at least, those are my own crazy theories on the subjects at hand. *shrug*