I'm just going to quickly go through everything in chronological order. If it's not on the list it's because I didn't watch it, or I didn't watch all of it. Probably because it was just a big load of crap.
X-MEN - Stupid and dull, despite its fine casting, the film lacked any sort of villain or storyline, claiming it was being 'saved for the sequel'.
UNBREAKABLE - A surprisingly gripping movie with lots of subtle elements that create a palpable mood of tension.
BLADE II - Nothing particularly memorable but not awful or anything.
SPIDER-MAN - Almost a great film, but unfortunately the Green Goblin (not Norman Osborne) was lacking, it was too long, and the ideas within it just aren't sustainable for over two hours.
DAREDEVIL - A light, fun movie that unfortunately skipped over a few key scenes far too quickly and had a lackluster ending, but had terrific villains and good arc for the hero, but it was ultimately scuppered for acting like it was much darker than it was,
X2: X-MEN UNITED - The sequel refuses to pay anything off as it drones on about Wolverine's origin, and instead of having anything remotely interesting happen, it just sets up new characters and villains for the 'final part of the trilogy'.
HULK - An almost brilliant film, with every single creative decision done right, and with a fantastic CGI Hulk, that completely falls apart due to an incredibly boring opening half-hour and an equal idiotic final half-hour, which is all the more upsetting as a simple MEN IN BLACK type of re-edit would fix the film entirely.
THE LEAGUE OF EXTRAORDINARY GENTLEMAN - A stupid, nonsense popcorn blockbuster with no charm, substance, or thought, despite having Dorian Gray who was pretty cool.
HELLBOY - A wonderfully light, simpler take on the comic book version that's very entertaining, but the film fails due to it having the bad "alternate ending" to BLADE.
SPIDER-MAN 2 - In a desperate attempt to make it more sustainable, an idiotic number of sub-plots are brought into the movie and never have any purpose or meaning as Sam Raimi pretzels in random elements of the comics around a paper-thin plot, despite having a kick-ass villain in Alfred Molina's Doc Ock.
THE INCREDIBLES - As is the case with Pixar, this film is a complete gem; not only does it have wonderfully realised characters and a fun world to put them in, it actually has a substance behind the spectacle, showcasing the mid-life crisis of a man who begins to resent the life his family has created for him, as well as the burden of potential and the celebrity of mediocrity.
BATMAN BEGINS - Much like HULK, there isn't a single creative decision wrong with this movie in any area, yet, bizarrely, the result is a rather tedious, boring movie that, while somewhat entertaining and intriguing, spends all its time dancing around the fact that its about Batman rather than just embracing it, and ultimately coming off as a worse version of BATMAN: MASK OF THE PHANTASM.
FANTASTIC FOUR - Put to shame by THE INCREDIBLES, a more appropriate name would be "Mundane Four" since the climax of this movie involves the super-genius Reed Richards defeating a neutered Doctor Doom with GCSE-level chemistry.
V FOR VENDETTA - Completely missing the point, the movie embraces bullet-time spectacle over the actual substance of the comic, neutering any elements of the dystopia and the characters, turning it into popcorn action and a totally bizarre ending where all the anarchists wear the same exact costume.
X-MEN: THE LAST STAND - While chaotic and rabid, and singularly stupid in missing key plot points that would've developed a better ending, the movie is genuinely surprising as things actually happen: major characters suddenly die or otherwise removed from the story, while at the same time, balancing all the major characters so it becomes an ensemble cast, making it the only X-Men film I enjoyed.
SUPERMAN RETURNS - The movie has some excellent Superman moments in which he rescues people and it definitely has some charm in using the Williams score and Spacey as Luthor, but making him a stalking father of an illegitimate asthmatic child doesn't gel with the whole "Jesus" angle the film stupidly tries to give him as he struggles against a big kryptonite rock that miraculously works only when the writers want it to.
300 - A fantastically operatic action movie, it plays itself so far over the top that it becomes rousing, creating a rush of adrenaline few action movies ever achieve.
SPIDER-MAN 3 - Combining the worst elements of the previous two films; a lack of sustainable story, too many sub-plots that go nowhere, and idiotic villains, this film goes on for three hours with the main superhero crying like a baby throughout, while all three of the villains turn out to be non-events.
IRON MAN - An extremely entertaining film with incredible charm and charisma, it is the best television pilot ever made - it lacks the completeness to really be a 'movie', focusing too much on creating a franchise rather than being a complete artifact in and of itself.
THE INCREDIBLE HULK - Replacing Ang Lee's choice for a more emotional film, this goes for the equally valid high-octane action, but unfortunately, while everything Ang Lee's film failed in this one got right, it messed up everything Ang Lee's film got right, removing a lot of the emotional investment in Hulk and the CGI quality resulting is a film that is perfectly entertaining - except when the Hulk is on-screen, resulting in a mirror-image.
HANCOCK - An unequivocal success and a fantastic new superhero, extremely engaging and fun, right up until you discover Hancock's origin at which point the film immediately collapses under its own weight and the whole experience turns to ash.
HELLBOY II: THE GOLDEN ARMY - Possessing a number of wonderful little touches, the film has absolutely no teeth and goes off in a completely bizarre direction as it gives Hellboy and Liz a child, spends time with Hellboy drunk-talking with Abe Sapien, and once again, has a rather poor ending.
THE DARK KNIGHT - Sublime from start to finish, the movie twists and turns with masterful pace and skill, continually surprising you and utilising every single element from the previous film into a fantastic climax.
WATCHMEN - A badly told wonder, the movie is bloated, incoherent, and far, far too loud in every respect to such a level that entire plot points are lost in the cacophony, yet the story and atmosphere are strong enough to actually make it mesmerizing in a wonderful way.
So... if I had to rank
10. DAREDEVIL
9. HELLBOY
8. BATMAN BEGINS
7. SUPERMAN RETURNS
6. UNBREAKABLE
5. 300
4. HULK
3. IRON MAN
2. THE INCREDIBLES
1. THE DARK KNIGHT
To be honest, #4-10 would probably change on my mood or whichever one I just saw, X3 would probably jump on if I had seen it recently. Anyhow, there is a big difference for me between #4 and #3. The top three are wonderful.
If I included movies from outside the 2000s, the list would be...
10. 300
9. HULK
8. IRON MAN
7. BATMAN (1989)
6. MYSTERY MEN
5. THE ROCKETEER
4. SUPERMAN: THE MOVIE
3. BATMAN: MASK OF THE PHANTASM
2. THE INCREDIBLES
1. THE DARK KNIGHT
DICK TRACY should've been on my list because he has pretty much the best rogues gallery ever but it was played so campy it just didn't work right, as opposed to the 1966 BATMAN which did camp wonderfully.