For me it would have to be Heatran. Also He/she is the worst Legendary as well. It's the only legendary with gender and It's only in one or two games so it's even tougher to catch. Over I absolutely hate Heatran! He is the hardest to catch and the worst Legendary ever.

The lowest catch rate in the game that isn't 0 would be 3, and most legendaries have a catch rate of 3. Therefore, the hardest to catch would be the ones that immediately run away from the battle.

Zapdos and the other elemental birds are the toughest because they always run away from you:'(  
  
Also Heatran is not nearly the worst legendary. His typing and ability are really quite good. I would say the worst is Regigigas .

A pokemon that is worse than legends.. Beldum. It has the same catch rate as most legends which is 3 aka 0.4% at full health with no status effects. It's only move is takedown so you can't false swipe. Basically you have to be lucky to catch one unless you are playing one of the 5 games(that I remember anyways) that gives it as a gift.

awesomeguy279 : When I said Heatran is the worst I didn't mean literally. He's just always sucked to me.

Actually, Heatran isn't the only legendary with gender, but that can be either female or male. You've got Latios and Latias with genders, for example, with them being male and female respectively.

The hardest for me has to be Abra. The catch rate is decently high but the reason I find it harder than other Pokemon that run away (like legendaries) is because most legendaries keep the status effects/damage you do to them. Abras? They teleport away so we never see them again. Only way to get one is getting lucky with your first Pokeball (which isn't too hard; I just have bad luck) or Mean Look or something to that effect.

Any of the legendaries that run away after one attack are all equally the hardest to catch. Unless you can put them to sleep over and over and over, you need to spend a lot of time trying to find them and battling over and over with a ton of trial and error until you finally get it right, and then after a while you run out of Poke Balls to use and you rage quit.

I agree with pokemon x that Beldum in Diamond/Pearl/Platinum is probably the hardest Pokémon to catch. With a very low catch rate of 3, and Take Down as its only move,  I can sympathize with anyone who has ever had difficulty in trying to catch one of them. In fact, I'm not entirely sure if I ever caught a Beldum in any of those games.

I say all or most legendary pokemons....they are really annoying to catch so you need to think in the best possible way how to go and catch them which would not be easy. So I always carry like 50 or 100 ultra balls with me just in case. :/

Legendaries that flee aren't that hard to deal with if you have a Pokemon with a move/ability that prevents escape. Like someone said you can just put them to sleep otherwise which should do the job as well. It's still pretty easy to catch one like crobat and just grind for a few levels to use it. I find the hardest part to be tracking them down which is really more frustrating and time consuming than it is difficult.

To me the hardest to catch was probably Mewtwo in the original R/B/Y. Reason being in the first generation games Pokemon balls could often miss when throwing it at a legendary. Couple that with him being the highest leveled Pokemon in the game and one of the highest leveled encounters in any Pokemon game. The fact that he's a psychic type which was broken until the 2nd gen games due to having no real counter with the highest special stat in the game and high speed. As well as having recover meaning he could heal back damage you did and he was a royal pain to get. If you're not well prepared it can very well end up KOing your entire team due to how powerful and hard to catch it is.