1. Civil War
2. Avengers
3. Iron Man
4. Winter Soldier
I don't really have a fifth. Those are clearly the best four to me. A lot of the others are decent but not great (The First Avenger, Guardians, Ant-Man, Iron Man 2, Hulk, Thor) and some are pretty bad (Ultron, Iron Man 3, The Dark World).
Civil War beats Avengers because there is a genuine sense of peril and a weight to the conflict - as well as a fun script. Avengers was great for two thirds of the film, but a final battle against a horde of faceless aliens got pretty boring. It can't match the emotional resonance of characters we have come to care about coming to blows.
Marvel is at its best when it balances the lighthearted, quippy stuff with more substantial themes and a sense of real danger. It fails when it gets this balance wrong - almost always because films are undermined when they are obsessed with not taking themselves seriously. Civil War gets the balance right.