Paxfish makes a good point. I'm constantly removing items from my boat that the Admiral thinks she just has to have aboard.
For the items that I've determined that I do need, I use a combination of 'Tupperwear' containers (sourced from Target) and soft-sided bags to hold and store common equipment. The Tupperwear keeps items such as chart books, cruising guides, manuals for the onboard electronics, insurance papers... that sort of stuff.
Fowl weather gear, dock lines, assorted cordage and rope hardware, safety items, sea anchor... this is the type of equipment that goes into soft-sided bags. Even my tackle bags are soft-sided. One for trolling, one for jigging, one for bottom fishing...
If its something that isn't needed, it gets taken off until it is.
That's the method I use.