This has been asked quite a few of times before. XD The two most logical choices, as far as legendaries are concerned, are Mesprit or Cresselia, as they run away from you when you encounter them, as well as have you play this game of tag with them as you chase them around the world map. The Master Ball would make at least one of those legendaries much less of a pain. Dialga has a higher catch rate, and should be easy to catch. Although...you do mean Palkia, right? Well, same deal.
But it is possible to catch Mesprit or Cresselia by weakening them slowly, or simply trapping them in battle so they can't run away. You could then also use the Master Ball on a shiny you're afraid of fainting, or it fainting itself. The only time I've ever used a Master Ball was on the Suicune in LeafGreen, as chasing it around isn't as easy or fun without the little Pokétch map. =/