PokéBase - Pokémon Q&A
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There are many Pokemon who share the same lowest catch rate of 3. Almost all legendary Pokemon have this catch rate, along with the Beldum line.

Source: http://bulbapedia.bulbagarden.net/wiki/List_of_Pokémon_by_catch_rate

Of course Event Only pokemon could be considered more difficult. Not only do they have a catch rate of 3 (if they can be encountered in the game). You must be at the right place at the right time (some event) to get them. (Arceus, Shaymin, Darkrai) Just saying...
Also don't forget Moving pokemon like HG/SS Entai, Rakiu. Black/White Tornadus/Thundrous. These pokemon run as soon as it's their turn. Very annoying trying to catch them. Same catch rate of 3 but you have to encounter them like 20 times to be successful.

Perhaps that makes Landorous the most difficult to catch. You have to catch moving Pokemon Tornadous and Landorous. Bring them to sacred shrine. That Catch rate of 3 each so... yeah.