Iris KP-XLPHO Photo Keepers for my sub-Constitution-size ships (2 ships plus bases, logs and decks per photo case, 16 of those per outer case--the limiter here is maximum yard width--32 small ships stored per case), Really Useful Products 0.3L Organizer Packs for everything from Constitution up to the largest two-deckers including decks etc (limiters here are sparred length and height from waterline to masthead; one tray holds 16 one-ship boxes), then Really Useful 0.7L boxes for the three-deckers at two per.

Starter ships I keep in the Starter boxes, and one of my two groups of Kickstarter Exclusives has been packed into a surplus Starter box Eric gave me along with a Counter Set and Mat set to create a "home-brewed Kickstarter Edition Starter".

Total:
1 Photo Keeper (two spares set aside for future expansion and miscellany)
3 SGN Starter Set boxes (diligently seeking a fourth)
1 Really Useful 0.3 Organizer Pack (need to pick up another one or two for Waves 3 and 4)
7 Really Useful 0.7L boxes (need to snag 3 more for Wave 3)