I have found the 12X9X6 to be the most versatile size. You can fit up to 2 hatchlings in deli cups in the box, or up to 4 smaller or 3 larger hatchlings in bags. It's also not too excessively large for a single hatchling in a deli cup, and it provides plenty of protection when you stuff it well with newspapers. Smaller boxes I think would be more likely to fall or be handled roughly.
By the way, ULine also makes insulated boxes. The foam is actually molded, and slightly thicker. They are higher quality, but they're also a bit more expensive.
http://www.uline.com/BL_2157/Insulated-Shipping-Kits
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