I always thought a soft bag would be better than a hard box due to the unusual shape of the limited storage areas. During my first season on the boat I used this cheapo bag from Harbor Freight:
...but as the year went on and more tools made a one-way trip from my house to the boat, I needed more room and a heavier, more durable bag. After a lot of shopping around, I went all-out and got this sizeable, very hefty bag from Home Depot:
I really like the tool wall in the middle and pockets around the side, because I can see all the tools from above instead of having to dig through a pile. The heavy rubber feet prevent the bag from sliding off the cabin top when I need to take the bag topsides.
As for moisture prevention, I assumed that silica gel and other small preventers would not last inside the bag because of the way the bag breathes. The solution for me was to minimize moisture throughout the boat with a dehumidifier when on shore power, and DampRid canisters when on the hard. I've posted about the dehumidifier in another thread
. Since I'm just a daysailor, I don't spend enough time at sea to worry about moisture while away from shore power.