I use large freezer bags (more durable) for each of my sets. Within that set bag I use a small storage bag for the minifigs and accessories. Large base plates are labeled for each set. All of my extra bricks are seperated in storage bags by color. All extra minifigs and accessories are seperated by theme, ie, Castle, Pirate, etc. All this fits nicely in storage bins.
I use a combination of items. Sterilite offers a varitey of storage products to suit my needs. Checkout the 'Clearview' storage items from Sterilite. You can find these at your local Target store. I also use arts and craft cases that have expandable compartments/dividers for the smaller items.