I only sleeve cards that are in decks. For this game, FFG silverlines because they are clear and I like the way the Netrunner backs look. Loose cards go in vertical oriented boxes and are sorted by faction/type/alphabetic order with labeled dividers so finding the card I want is never an issue.
Decks will go in red and blue Rook deckview capsules:
X2 each of blue/red is enough for main decks. Black deckview capsules are good enough for any other fun/b-decks. I like the plexi-window because it provides a visual of the Identity card. The tokens and other game amenities will be stored within the ziplocks that came with the game inside regular capsules; credit tokens in one, the rest in another.
The capsules are carried in one of these:
Rook cases are steel, so when fully weighted with cards they are ideal for braining potential muggers. Since the case is big enough to hold 16 Rook capsules I will most likely carry extra cards I am looking at possibly swap into decks (like sideboards) or maybe even the complete collection until it gets large enough to warrant the big box.
EDIT: I agree 100% with prune about cardgamedb. This will be the third LCG I have picked up that will benefit from the site's tech.
that Rook carrying case is pretty slick.