From SciFi's official clue site You Will Know the Truth, by my count there are 3 outstanding clues yet to be addressed:

Clue 6 - Head-Six asks Baltar, "If you were one of the Old Gods, which one will it be?" (video clip)
Clue 7 - The Last Supper image minus Roslin (still image) - she ain't dead yet
Clue 11 - Twelve tolls of a bell (audio clip)
... and possibly a fourth clue (Clue 16), a scratchy audio clip which I deciphered to mean "Do you remember what we said on New Caprica?" - sounds like Six or Kara)

Further, there are several huge questions left outstanding:
-The meaning of the Opera House visions, and possibly the Opera House itself from the Kobol days
-The power orchestrating all of it - we've been told again and again that someone or some thing is pulling the strings
-How did Kara come back? And what is she?
-Who built the Magic Viper?
-The meaning and nature of the Head characters

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