A lot of people seem to be saying in this thread that because Section 31 is not 'constrained by morals or accountability' that it is inherently more effective. It's far more likely that it ended up being, for those of you who've played Mass Effect, Cerberus. An organization led by a man who substitutes his own political feelings for the 'Best interest' of the Federation.
^Well, recall how in "Extreme Measures," Sloan implies that there is no "central" leadership per se for Section 31--that there are cells run by members of a "select few"--Sloan being one of them. (This is referred to in the VOY Section 31
novel wherein Sloan is referred to with the title of "Director". Other "Directors" in the novels would be L'Haan, Cole, and Zeitsev.)
In a fanfic of mine (which you can find on this site, "Our Sacred Honor") I depict The Bureau as made up of Divisions, each run by a Director, who periodicaly meet together to discuss the Bureau's response to a current crisis. Thus, there IS a kind of "internal" check-and-balance system. But again--that is my interperetation of the facts we've been given.