National Bank: Still one of the best first NIs, esp. for the time before you get (overpowered) Master of Mints.
Bill of Rights: Only good for the CB.
Bureaucracy: The worst NI of all. Really.
Merchant Adventurers: Useless. The other trade NI are better - and if you are losing that many merchants, you need the other ideas, if money is a problem... Err...
Shrewd Commerce Practice: Good if you have high infamy, but usually NTP is better. Good 2nd choise for trade nations.
National Trade Policy): Best first NI for trade nations. Adds 5% compete chance and increases trade income during the early game by roughly 30-50%. Very strong.
Espionage: Good against large empires, esp. during the later stages of the game. Fabricate Claims is nice to "catch-a-throne", rebels - esp. pretenders - can wreck havoc if used correctly.
Ecumenism: Nice to have during the reformation. Dunno if it still speeds up conversation events for protestantism / reformed. If it does: Neat!
Humanist Tolerance: Rather weak, but at least better than BoR. Situational idea for multicultural empires.
Unam Sanctum: Weak CB, but at least papal influence. Only good for papal control strategy.
Church Attendance Duty: Stab cost reduction is rather good, papal influence is nice, decent NI for
Divine Supremacy: Rather weak, only useful for papal influence.
Cabinet: Very strong NI, although very late. Still, great for late game conquests!