Best: Either Paper Mario or its sequel. If I had to choose one, I'd choose Paper Mario: The Thousand-Year Door. He just looks really good in that sharp-lines cartoony look, and in hindsight, it was good in the first game when he was laughing after defeating Mario at the beginning, just to give him a bit of a light-hearted personality. I mean, whenever Bowser does not look imposing or superior or macho, I like him.
This is a good example of what I like. Again it may be the choice of a cartoony look, or that he looks cute and somewhat ridiculous rather than fearsome.
Worst: Tossup between Super Mario Sunshine or Super Mario Galaxy, but I'll give the disgraceful nod to Sunshine just for giving him a lame voice with English words. Look, if you're going to make him speak English, he'll have to be a lot more like the Bowser in the cartoons so it doesn't come off as awkward and embarrassing. I rated Super Mario Galaxy as second-worst because I don't like Bowser when he has that detailed bump-mapped shiny reptile skin. Jibblie jibblie.
Cartoon version of Bowser was pretty good too. Sure, he looked more like an artistic representation of his self from the first Super Mario Bros. game, but they made that work. Gave him a good voice, a funny personality... see, that's all I ask. The Koopalings meanwhile were sometimes on the creepy side, I just didn't like their cartoon selves as much as Bowser.
By the way, I just remembered seeing the
Mario Power Tennis Bloopers on YouTube. Half the time it comes off as unfunny and uncomfortable, but there's some good bits. Bowser's more light-hearted here (someone remarked he does a rare non-evil laugh). We've seen the range of emotions that can appear on characters in Star Fox Adventures, Beyond Good & Evil, Half-Life 2, and so much more. Oh, and recently Zelda: Twilight Princess. I really want to see Bowser get more animated and have more of a personality, but I guess for now we'll have to rely on his Paper Mario appearances.