Interesting choice of movies, all somewhat popular, all imperfect, but all have some similarities...for starters, they are all from well known established universes, though STO9 was a first movie reboot. All are nominally sci fi (yes even DKR). All are blockbusters (yes even Prometheus).
My picks in order:
1. STO9: Whether it's like TOS is the least of my interests here, however, if you ask this question you may get 10 different answers from 10 different people. In general, its almost shocking how WELL they adhere to the original characters, Pine is sometimes uncanny as Kirk without slipping into caricature, which would have been exceedingly easy to do. They also got the adventure right. As for the more important stuff, does it work as as sci fi movie? Drama? Is the action good for an action-adventure? Yes, in my opinion ST09 is actually better than any of the SW movies (which it sometimes is compared to), especially the prequels which it trounces on every level in my opinion. Dramatically, it takes characters with little background and immediately draws them very sharply, it is literally designed to show us character growth through the likely JJ Abrams trilogy of movies. I find this refreshing for ST movies! Well there is reason this movie won awards for its WRITING, not just from sci fi circles but also from the mainstream, in fact, the awards were unheard of for ST movies. Add to this the high scores from aggregate sites online, and it's clear ST09 was a huge success. Financially, it made over $500 million from BO and DVD/BD, taking trek firmly out of the niche market. There are few weaknesses here.
2. Prometheus. I really enjoyed this movie...though it IS highly imperfect. I feel it was mostly executed exactly as the writers and producers wanted it to be, though I do not believe in ancient astronauts on Earth, I find the potential reveal of the speculated on origins of the Engineers and their masters along with the connection to the Aliens themselves to be worthy of a sequel that I am eager to see. Far from ruining the previous two good Alien movies, I think Prometheus deepens them. Alien was gothic suspense in space, Aliens was military SF, Prometheus was high concept sci fi, with all the other elements thrown in.
3. DKR. I loved Dark Knight...I could quibble with some issues in it, and it was overly gratuitous in its violence, but the movie was more of an experience rather than just entertainment. One would go into DKR expecting much of the same...well DKR didnt seem to make a lot of sense. Most action movies have some inconsistencies, or failed logic, failed science, but DKR had too many to really make it a great movie. Fans of Nolan will of course probably check this off as the best of these three movies by default, but its easily the most flawed of these 3 films.
One more note, it is now easy to see that Christopher Nolan is the most influential Director-Producer of our time. His choices from music, to plot, etc is widely copied. Despite the flaws, DKR will probably continue his reign.
A word about trailers...I mentioned ST09s third trailer was the best I'd seen, tuned out that trailer won several awards amd is still talked about in regards to effective advertising for films. If you didnt like the 3rd trailer then there is no hope for some of you.