Gotta give it to Bowser here.
I can't think of too many characters, much less villains, who are able to flow between two main archetypes (imposing, menacing badass, as well as the lovable oaf) so well, from game to game. Hell, in the recent M&L3, you could argue he did just that within the context of ONE GAME.

The best thing is, it just "works" and is seen as something that works well with the character. For example, I couldn't see the likes of Wario and Dedede being "bad-ass threats", any more than I could see Ganon(dorf) or Ridley being relegated to "comic relief". If you were like me, trying to imagine such would likely make your head hurt. The notion of such would likely cause a conflicted image of what you perceive the characters as. Yet, Bowser is able to walk this thin line of "believe-ability" and do it well.
Plus, you gotta give it to a guy who runs a highly industrial Empire with efficiency, and seemingly has enough charisma-inspiring loyalty that his minions follow because they WANT to, not because of the usual "you know the price of failure...!" type of thing that can be so normal for a lot of villains in any medium. Even his brat pack (canonically, in the games, at least) don't seem to have any interest in trying to usurp his throne, seemingly content to let Pops stay in charge. The fact that Junior went through the trouble of resurrecting his Pops, instead of taking the throne for himself (when he certainly could have) speaks to me a lot.

So, for him being in the business almost as long as Mario himself, I think that Bowser deserves just as much credit as the man himself. Because after all, a hero only remains as great as the villain(s) he combats, right?
Runner-up: POKEY/PORKY (Mother series). From being the annoyance in Mother 2/EB, to a megalomaniac that made me actually love to HATE the guy in M3. This guy caused a lot of strife for many people in the Mother-verse, and did it in a way that just showcased what kind of guy you were REALLY dealing with all along. Bravo to Itoi for excellent writing regarding this guy.