I was assuming that a team would challenge the Yankees. Maybe not.
Unfortunately, I think the answer is the New York Yankee organization. In 107 years, the Yankee organization has a total of 26 World Series crowns (roughly 24.3 %). I would think the Marlins are right up there as well...they've won 2 championships in 15 years (13.33 %).
I'd be curious to know how many baseball fans realize that the Yankees started out as the Baltimore Orioles?
Bringing another sport into the discussion, the NHL's Montreal Canadiens have won 24 Stanley Cups.
http://en.wikipedia.org/wiki/Montreal_Canadiens
The D-Backs once did hehe