For storing them at home, I store them in Acro Mils Large Storage Bins, shown in attached pic (don't be fooled by the "Large" title - they're only about 14" x 10" x 2"). If I'm taking a whole bunch somewhere, I'll leave them in their bin and take appropriate bins with me. (I have thousands of the plastic suckers now, so bins are marked are thematic by type: "Aberrations", "Orcs", "Goblins", "Human Fighters", "Magic-Users", "Spiders", etc.)
If I'm taking only a few with me, I'll toss them in a plastic bag, or if I'm taking enough to matter, I'll use multiple bags to separate the different types, and maybe throw the bags in a hard plastic case (like a shoe box sized one).