Assuming the Sinister Six would be vaguely analogous to Spider-Man's original Sinister Six, I'd say:
Mr Freeze (Octavius- tragic scientist genius figure).
Scarecrow (in place of Mysterio. The link's a little tenuous, I know).
Man-Bat (in place of The Vulture).
Killer Croc (vaguely equivalent to Kraven).
Clayface (clearly, corresponds to Sandman).
Maxie Zeus (Electro).
Joker won't be in a Sinister Six because Batman's Six would cooperate together to make life hell for Batman- the Joker strongly believes that only he has the right to mess with Batman. This was scene multiple times in comics, and hell, even in TDK, he threatened to kill that dude who was gonna reveal Batman's identity. He would never agree to work with any other supervillain long-term, except for Harley Quinn. And hell, the Joker nearly killed her when she was going to kill Batman.
Batman's 'Sinister Six' would undeniably compose of six of Batman's lower a-list and b-list villains (no Joker or Ra's-al-Ghul-class, but no Calendar Man-class, either). I'm thinking either Black Mask or Penguin, Killer Croc, Two-Face, Mr. Freeze, Clayface, and Man-Bat.
Originally posted by Markus Corvinus
Ra's Al Ghul wouldn't be leader, the Joker wouldn't allow it. I know he's not a team player to begin with, but he'll kill for leadership, if he intends to be on the team, that is.
Exactly... Either he's leader, or he's not in it... That's his mentality...
And Two-Face, I can't see wanting to join... He's got his own problems...