Best external SSD solution

I am planning on getting the new iMac with the 256gb SSD. I will need a larger drive than that, but rather than paying apple's markup, I would prefer to get an external SSD. Am I better going with Thunderbolt or USB 3.0? I assume that the red/write to the external will be slower than to the internal. Suggestions for which files and folders would be best on the external?