We put all our action cards into nine-pocket-pages, organized by the skill used for the action. For the most part, you want actions you're good at, and those yellow dice sure are dependable. Seemed like a natural way to divide it.
It made searching for a viable action for a given character really easy. Having just 3 categories (Ranged / Melee / Support) meant there was still a ton to look through and really took time to find anything. Having a tabbed page for each skill makes it much quicker and easier at the table.
A few of the actions had more than 1 skill, or different skills on each side. When this happened, I put them in whichever skill had the fewer actions. The last pocket on the last page of each skill has a little piece of paper listing actions filed under other skills that might be worth cross-referencing, as well listings of talents that boost specific skills, etc.
The biggest section was, unsurprisingly, Weapon Skill. So I subdivided it further. Any attacks that gave a bonus fortune die if you had some other skill trained went in that skill's section instead. Then I made a page for the handful of actions that use Weapon Skill plus something other than Strength (usually Agility). As the final sort, I made seperate pages for actions that require specific weapon types. Here's the great weapon actions, there's the weapon in each hand actions, and that page is the weapon plus shield actions. Bla bla bla.
Within the various pages, I don't worry at all about alphabetizing. The categories are small enough I don't really need it.
For spells and blessings I did the same, breaking it out by Faith or Order, then by Rank. In fact, I put the Rank 2+ actions, all the Epic stuff, and anything overpowered in their own binder until after character creation. That way I didn't have to worry about the players accidentally using it before I felt the campaign was ready for it.
The whole process took a lot of work, but it really made character creation a breeze. It's also greatly simplified Advancement and just generally looking things up. I'm almost always willing to trade GM effort between sessions for ease and elegance during the game. Plus, my wife gets this weird thrill out of organizing things, so I totally didn't have to go at this alone.