At this moment (up to Voice of Isengard expansion and CORE NIghtmare), i have the cards so:

One file are quest cards and player cards (and dials, and tokens), and second pile are encounter cards (not quest cards because there are no place for them!).

You? How is your box(es)?

My player cards are in binders (5) and the quest cards are still in the original boxes stored in a large chest.

I have all my cards in a big box that latches shut, and all the cards are in individual boxes (some that hold 50 cards, others that hold 150). I usually have them sorted as individual quests or player decks for the little boxes, and the big boxes hold entire cycles or all the cards in one sphere. Did that make sense?

I have all my player cards in this insert by Mr. Craft and it's amazing!! I have everything except VOI and in the center of my box is the core encounter cards and a couple Print on Demands. For all my other encounter cards they are in their original boxes. So this box keeps all my player cards, tokens, etc. nice and organized.

Check out this link for other card storage ideas.

There is also go7gaming but I don't know much about them.