Well first Travis Touchdown because he's actually a character and not some stereotype or drawing that just kinda fills a part. He really serves a purpose in the game and the game wouldn't be No More Heroes without him.
Second I would have to say Jack because just like Travis, the game is made by him and can't be replaced by some generic character. REally fills the part.
Finally of course is still my two favorite characters of all time. Sure there games were also on last generation systems but have to include Leon Kennedy and Link because I can haha: