Assuming you're talking about Black/White, most of the legendaries have a catch rate of 3 (as in most games), except for Reshiram/Zekrom who have a catch rate of 45.
Personally I chose Thundurus/Tornadus because roaming Pokemon are annoying to catch! Not just the fact they flee but trying to find them in the first place takes a lot of time. So just chuck a masterball and be done with it.
But if you already caught those... you can save the masterball for a high level legendary. There may be some coming out in the future through events. Often you are just given event Pokemon through Mystery Gift, but some (like Darkrai and Shaymin in Platinum) you need to catch.