One idea I've had is to create a movie trilogy surrounding the Hero of Time. The first movie would be the child portion of Ocarina of Time; the second would be the adult portion; and the third would be all of Majora's Mask. With OoT being by far the most iconic Zelda game and MM being a strong continuation of its protagonist's tale, I see it as a nice fit for a movie series.
I'd extend OoT into two movies, simply because of its length being neither fit for the two to two-and-a-half hour movie time frame nor comparable to the much shorter MM. Another thing that would need to be fixed regarding OoT in the transition to the big screen is character interaction, especially in the latter half of the game; there's some with Sheik and the Sages but little else, and I think that would need to be changed in order to not be boring - OoT was able to pull this off the slight barrenness as a video game, but wouldn't be able to as a film. Going along with this, the temples would have to be rather profoundly edited, in order to retain a reasonable length and keep the audience's attention. The last thing I'd change about OoT is I'd give Ganondorf - and perhaps some other characters - more screen time; this would provide an aforementioned bolstering of character involvement that I think would be necessary in an OoT movie, or any Zelda movie for that matter.
As for Majora's Mask, it could stay how it is primarily. Its characters were much better involved, though the question would be raised of which sidequests could be incorporated into the movie. Also, the times at which the Song of Time is used by Link would need to be figured out, but that is a rather minor issue. As with OoT, the temples would need to be condensed, especially with the somewhat prodigious length of MM's temples. Another thing related to my OoT suggestions is that Skull Kid should be given more screen time; I'd also recommend allowing some of the in-game sidequests to play out on their own without Link, just to give a short, refreshing break from his storyline and focus on the distraughtness of all of Clock Town - similar to the events in Gotham in The Dark Knight Rises.
With these changes incorporated in development of the movies, they could really play out nice. To make another connection to the Dark Knight Trilogy, I think the films would need a realistic tone to be successful, though this could be executed with either CG-animated or live-action movies. If all or most of that was implemented into a film trilogy based on the events of Ocarina of Time and Majora's Mask, I think it could result in an incredible production.