Quickest way to mass transfer pokemon?

[Tsujin]

So recently my entire case containing my DSi, Acekard and all of my physical pokemon games (Pearl, Platinum, SoulSilver, White, and Black2) was stolen and is gone for good. Now this doesn't bother me too much since I still have my 3DS and X version but with Pokebank coming up I'd still like to be able to transfer what pokemon I have left since I was always careful enough to backup my save files from each game. Now my question is what's the best way to mass transfer pokemon that were in my 4th Gen games and get them into a 5th Gen game to be ready to be transferred.

Now as of right now I have save files of all my games and the .pkm files of all my pokemon as well. I need to get these 4th Gen .pkms onto my White Version save file but in a legal way so they look as if they were transferred over normally and not just thrown onto the save file as they are right now. Once I have all my pokemon back and onto 1 save file (being my White save file) I can put the save file onto a physical copy of White to transfer via Pokebank. So what's the best method or program I can use to "transfer" these .pkm files and then put them onto my White save file?

[LEGOanimal22]

You could use PokeGen or Pokecheck.org