Plano trays for mine, stored in a wheeled duffel bag from WalMart. Ten trays, two for each faction, one for tokens and templates, one for the Epic stuff (including the GR-75), and two for my son's collection. A smaller tray holds the mission tokens. A larger tray holds the larger ships - the Ghost, Shuttles, VT-49s, etc. That tray fits in the lower compartment of the duffel.
Pilot cards go in a binder, with most ships getting their own pages (or multiple pages if needed). This binder fits in the lower compartment with the large ship tray. Upgrade cards go in their own binder in the pages sized for them. This binder fits along the side of the trays in the main compartment of the duffel.
So I can get my entire collection in the one bag, with the exception of the rest of the Epic ships which go in a shoebox that they fit neatly in. The only problems I have had with this storage are the b-wing cannons. The ships don't move enough to damage themselves as long as the compartment they are in is snug enough.
I have seriously considered the Battle Foam, but I just can't justify the expense given the lack of problems I have had with Plano.