I have found what I consider the perfect solution, and I doubt I will ever do anything else for any LCG games.

First, my requirements:

1. Use the Core Set box to hold the components.  There are around 100 board games on my shelf including 5 LCGs now, so I need to have the name of each game clearly visible.  Since the Core Set boxes all have great artwork and large titles it is ideal

2. The solution needs to be able to hold lots of sleeved cards, including the tall FFG sleeves in some cases.

3. The solution needs to be elegant, convenient (to take decks in and out, etc), and look really good.  I want to impress other gamers.

(Note: low price is not a requirement)

SOLUTION COMPONENTS (storage solution price is about $40):

8x Ultra Pro Acrylic Deck box, clear plastic, 100 sleeved cards.  Only TOP is used from each box placed upside down to create 8 open trays in the box.

1x 400 count cardboard deck box (unsleeved cards only).  Top flat cut out for open access if the core set box is opened.

SOLUTION: Once you have the components above, your task is to fit them in the Core Set box.  There is only one way to do this, and you will see that it fits perfectly.  

I have Lord of the Rings the Card Game with all expansions and it fits everything that we need to play (some scenarios left out of the box since we are done with them).  I will post some pictures to emphasize the perfection of this solution.

Well, what I ended up going with is picking up two FFG deck boxes, one each for Runner and Corp. I sleeved the cards in the deck and then put the rest of the cards, sleeveless, into small, cardboard card boxes. All the tokens went into a plastic card box, and then all of that, along with the rule book, fit into the original Netrunner box after taking out the insert. There is still room for a third card box if I need it, unless I can find a pair that are the same height and width, but a bit longer. Ideally, I'd like to have 2 card boxes that are the length of the box to either side, with the FFG deck boxes and token box in the middle, but what I have going now will work for quite a while.

I have found what I consider the perfect solution, and I doubt I will ever do anything else for any LCG games.

First, my requirements:

1. Use the Core Set box to hold the components.  There are around 100 board games on my shelf including 5 LCGs now, so I need to have the name of each game clearly visible.  Since the Core Set boxes all have great artwork and large titles it is ideal

2. The solution needs to be able to hold lots of sleeved cards, including the tall FFG sleeves in some cases.

3. The solution needs to be elegant, convenient (to take decks in and out, etc), and look really good.  I want to impress other gamers.

(Note: low price is not a requirement)

SOLUTION COMPONENTS (storage solution price is about $40):

7x Ultra Pro Acrylic Deck box, clear plastic, 100 sleeved cards.  Only TOP is used from each box placed upside down to create 7 open trays in the box.

1x 400 count cardboard deck box (unsleeved cards only).  Top flat cut out for open access if the core set box is opened.

SOLUTION: Once you have the components above, your task is to fit them in the Core Set box.  There is only one way to do this, and you will see that it fits perfectly.  

I have Lord of the Rings the Card Game with all expansions and it fits everything that we need to play (some scenarios left out of the box since we are done with them).  I will post some pictures to emphasize the perfection of this solution.

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.