Ok so the best punch is inevitably the one that suits the situation.
However, straight punches are slightly faster, have a longer reach, are less telegraphic, disturb your balance less and are less likley to open you up for counters. This makes them the main punches to use when entering from outside the boxing range, and there are many opportunities to land them from within this range too.
Hooking punches work best when you are closer to your opponent and gives you the option of hitting from all angles instead of straight forwards. This increases the amount of work and sensory information your opponents brain needs to take in if he is to defend himself, it also makes him less likely to pick the right defense manouver.
To be honest, I wouldn't say that one is better than the other, more that they are the compliment of each other. You need to master both, because if you haven't you can bet your bee-hind someone else has. For me however, I find that if I'm landing straight punches, I'll throw less hooking ones.
If however I absloutely had to pick a punch from my arsenal that has been most effective for me, its gotta be the jab (in jkd its the leading straight right).
Sticks n stones'll break my bones, but if I land the first one, you're in trouble!