Beedle has always been a classic for me. Friendly to his customers (for the most part), sells useful stuff, and gives good customers special promotions. Something about that "OOOOOOOOHHHHHHHH" and the "BYE!" makes him a delightfully charming character. I like that he's one of the only prominent shopkeepers that actually has character.
But, when one talks about character, one must also mention Malo. Though he was arrogant, sarcastic, and rude to his customers, he was a brilliant shopkeeper who knew everything there was to know about running a successful business (despite being, like, 3 years old
). He definitely has a personality, and the stuff he sells is top notch.
In terms of usefulness, I'd probably give it to Rupin, but he creeps me out so I don't like him.
So ya, overall I'd say I like Beedle the most, because he's become such an icon now and he's lovable in all his appearances.