I will also mention that it will be completely impossible to move pokemon from gen1 or 2 to any higher generation. I dont know much about it, but if its an exe, you can use wine or vmware to run it on osx. And then transfer them legitimately to gen 6. However, if you have access to a physical gen 5 game, you can inject your emulator sav file into the physical cart using a variety of methods. This is because pokemon are stored differently from before and there is no easy way to transfer them over with that method. You will not be able to move pokemon from gen 5 to gen 6 using an emulator. (There are different pokesav programes for each game). And just import it into the sav of the gen 5 game using pokesav. Once the pokemon is in gen 4, it should be easy to extract the pkm file from the gen 4 sav file using pokesav.
The following method may also work to move from gen 3 to gen 4, but im pretty sure gen3 pkm files arent directly compatable with higher generations.
Long answer: See daxtsu's answer above about using your emulator to link games. Short answer: As long as youre working with generation 3, 4 or 5, its possible.
