the differences are minor, BUT, they do usually say that the triple channel kits are tested together and stable. i don't think it should make a difference, and i'd personally go with whichever is cheaper, but it's something to keep in mind.
No difference. As long as they're the same ratings (voltage, frequency, and CAS).
Edit 1: "matched" sets might overclock better, depends on how the company did the "matching", you can only overclock to the point of the slowest DIMM in the set.
Edit 2: and you are usually better off using 3 DIMMs not 6. If you need 12Gb of RAM go with a 3x4Gb kit.