Actually, "It was the least I could do", or the even simpler "It was nothing." is a way of making the recipient feel at ease that they do not need to reciprocate.
If you tell them "It was the best I could do", then you're laying a huge guilt trip on the recipient that you've done the best that you possibly can do for them, and they will feel forced to return the favor. Which is not very polite.
@ Ingmar: Although I never use that phrase myself, I do understand that it is an abbreviated way of saying, "Given how important you are to me, I could not possibly have brought myself to do any less for you."
I'm guessing Dilbert did the same for Dogbert... present-wise.