Can Alchemists apply a poison to their bombs? Does the poison apply on impact and then boom goes the dynamite?
I would say you can apply contact poison, but not injury poison, as the hit with the bomb doesn't in and of itself hurt anything until it detonates. The bomb explosion does fire damage, and it's hard to put injury poison on fire. Of course, you can make the bomb poisonous with various alchemist discoveries (e.g. poison bomb). You can require the bomb to hit the target's normal AC and not just their touch AC to deliver the poison.
Even though they're called "bombs," the basic alchemist bomb works a lot more like alchemist's fire, it is a quick combination of reagents in a vial that makes a quick poof of fire and becomes inert in a round if you don't use it. However, it would seem logical that you could put the poison on the outside of the vial before beginning the bomb-activation process, so that doesn't seem like an impediment. As you mod bombs with discoveries, they can look more like traditional fragmentation grenades (scrap bombs) to super weird stuff (frost bomb, dispel bomb...).
An Alchemist can(at 12th level) get the ability to make poison bombs(that act as if a cloudkill spell).
However as to poisoning a normal bomb, it would actually be completely impossible regardless of anything else before 6th level as applying poison is a standard action and crafting a bomb is also a standard action. Since a bomb degrades unless thrown in the round it was created. It becomes possible at 6th only due to the Swift Poisoning ability.
I would also agree that only contact poisons would work as the others would likely get destroyed in the blast.
There does not exist any mechanism through which an alchemist can apply poison to her bombs. Let's consider each case, keeping in mind that bombs are thrown vs a creature's touch AC.
Contact poison will not work because there is no effective way to judge if a bomb thrown at a creature actually touches its skin. An enemy wearing a full suit of plate mail and a tower shield is quite easy to hit with a bomb, but virtually impossible to hit with a contact poison. On the other hand, a giant spider has no armor at all (but does the contact poison penetrate its natural armor?). So there is no consistent way for this to work. At best, you would have to convince your GM to let you use it on a case by case basis.
This one is even more unlikely, because it has all the same problems as a contact poison but must actually penetrate the creature's skin, not touch it. So by extension, it will certainly not work.
You could make a decent case for this one, if you were throwing a smoke bomb. There is no provision in the rules for it though, and honestly why bother? You could simply throw the vial of poison gas itself. It even fills a 10-foot cube, so it's practically like you threw a poison 'bomb' anyway. The only time this could be useful is if you wanted the effects of a smoke bomb and your poison in the same spot at the same time in one turn. A nice GM might let you do that.
If you can convince an enemy to eat one of your bombs, he has bigger problems than poison.
The alchemist's poison features are intended (as I interpret them) to be entirely distinct from her bombs. It would be overpowering to allow an alchemist to poison an enemy via touch AC and blow him up at the same time. It comes down to picking the right tool for the job; you can't have both.
I would say not. You can apply poison to weapons, but a bomb is not actually a weapon. In the same way, I would not expect to be able to apply poison to a Ray of Frost, or other weapon-like spell.
As a magus, you COULD apply poison to your weapon, and then spellstrike with it.