I use, mostly, Ninja Magic base adapters. All of my ships pretty much fit (off of the bases) in Sabol foam trays of various sizes. Once you have enough bases converted, they're universal, and you can buy adapters for additional ships in packs of 8. Not the most economical, overall, but I've found them to be MUCH more secure and less pain in the butt overall to convert ships because there's much more surface area to either crazy glue, epoxy, or glue-and-pin, as necessary. Unlike every other method I've used (and since 1985 I've tried them all), the NM adapters are the only ones that don't break ships and don't break bases.
For uber small minis, like corvette class through most destroyer class, I bought a ton of small rare earth magnets from ebay for less than $5 with shipping and glue one to the mini and another to the flight base with epoxy (make sure you orient the magnet the right way, and the SAME way for all of your ships. Ask me how I know!). Paint the magnet and/or adapter black to blend with the stand, and once on the table, it disappears.
I have plastic stands with Ninja Magic adapters, plastic stands for small ships, and the GZG metal stands with Ninja Magic adapters for large/heavy/unbalanced ships. They'll all fit in a properly prepared 2 inch foam tray.
I spent a LOT of time through the years drilling ships to fit flight base stems, fixing broken stems and drilling the broken pieces OUT of the ships, and ruining ships converting to jewelery barrel connecters.
The heart of all of this is the Sabol foam tray or equavilent. Lets you store everything flat, or in the case of the bases standing up where they're most stable. If you don't want one of the Sabol carriers, here's what I did=take a foam tray to Wal Mart and go back to the sporting goods department. Somewhere back there, especially in spring and summer, will be a soft sided cooler that will hold8-12 inches of foam trays for less than half of what you would pay for one that says SABOL on the side!
If you're very astute, you can get one that will hold a three ring binder of rules and have a pocket for dice and tape measures and pens, too!