HEAVY SPOILERS BELOW
I think Logan is one of the best ones. The acting is fantastic. It's plot is simple enough, following a familiar structure of a race towards a sanctuary and the character arc follows much of the hero's journey: Logan starts out in his daily grind, there's a call to action, there's a rejection of the call, there's acceptance of the call, he loses his Obi-Wan/Gandalf, he even has a literal conflict with himself, and upon defeating and coming to terms with his own fear/anger/savagery is allowed to be and act as the man he wanted but had failed to be, achieving the one thing he couldn't before: death.
Watchmen doesn't even register near the top for me. Zack Snyder hasn't made a good movie. Ever. (I'm willing to provide a more thorough explanation upon request.)
X-Men Origins: Wolverine has that really cool montage of him and Sabertooth rampaging through all the various wars. Other than that, the most memorable part is the Deadpool atrocity.
The Dark Knight is an average film carried by a great performance. But the Joker's plan makes no sense logistically and is almost too much for the suspension of disbelief to bear. Plus Nolan cuts a million times in every scene, which is a whole other level of annoying. (Other than convoluted nonsense that detract from otherwise good movies, his style of constant cutting is his biggest flaw.) Batman Begins has better structure. The Dark Knight Rises has a memorable villain but suffers from some serious flaws.
Superman is uninteresting. Every movie the villains pose no threat to him or they're Zod. Suicide Squad is terrible. Other than Batman, DC hasn't managed to make a good film using one of their major properties.
The Avengers has the best dialogue of any comic book film thanks to Joss Whedon. It brings together a lot of great elements including Loki. It has a consistent tone, good action scenes, and Loki's plan is simple enough not to become too convoluted. It's weakness is that it destroys NY for the 100th time and has a light beam rise into the sky for the sake of 3D, which is cliche.
Captain America: The Winter Soldier, Ant Man, Dread, Hellboy, and Blade are all just good movies, each achieving what they set out to do. But other than Captain America, which mixes the spy film elements, none of them attempt to heights beyond the typical comic book movie.
Sin City is stylistically interesting but lacks a sense of humanity.
Deadpool is both stylistically interesting and has a sense of humanity thanks to great performances by Ryan Reynolds and Morena Baccarin who especially helps provide an emotional core to the film. (More about it below.)
Guardians of the Galaxy is a fantastic movie, much in the same vein as The Avengers. It hits so many perfect notes and avoids the giant 3D pillar of light cliche. Like the Avengers the characters are charming, the bad guy's plan is easy enough to follow, and it has a sense of humanity and heart. It's failure is that Ronan isn't a memorable villain. He has none of Loki's charisma or the Joker's chaotic insanity. It's other fault (one shared with Deadpool) is its reliance on postmodernism. Whereas Deadpool's whole shtick is postmodern (meta fourth wall breaking, nonlinear plot, and an ironic detachment) which is at least consistent, Guardians flirts half-heartedly with postmodernism in scenes that call attention to comic book tropes, such as Rocket's comment about them all standing up in a circle. For that I detract a point.
But the best comic book movie is Scott Pilgrim vs the World: It is not cynical or ironic at its core but rather has characters who are cynical and ironic. Its relationship to its source text is intimate and sincere rather than attempting to distance itself from it through irony (think X-Men when Cyclops says to Wolverine: "Would you prefer yellow spandex?"). It embraces sentimentality: the action of the film is progressed by Scott's genuine desire to be with Ramona, and Knives' desire to be with Scott, and by the conclusion, the character's too have embraced a sentimental truth and the moral of the story. The nondiegetic elements aren't meant to pull you out of the experience, i.e.: the cutting and transitions are done in an interesting, obvious but narratively relevant way, the text and graphics on screen enhance rather than distract from the action. It is stylistically interesting and maintains its humanity through a sincerity of desire, friendship, and interpersonal conflict; Gideon's evil plan is simple but intricate enough to provide sufficient obstacles for Scott, Knives subplot offers a human obstacle to Scott and Ramona's relationship, and the Battle of the Bands subplot adds a separate set of goals and obstacles for the character to face, and manages to entwine these subplots with the main plot in interesting ways. As much as it cares about action, it gives a great deal of time to character. One of the problems with many comic book movies and action movies is that the Characters don't matter that much, they're just there to fight and be vague between tentpole action sequences. Scott Pilgrim avoids this.