I use four loose categories that sometimes fit a block better than others: artifacts, tribal, multicolored, and mechanics. The ones that are least fitting are tribal for Zendikar and Innistrad, but I think this label is close enough to decide how to pair these up.
The order as issued is:
1. Mirrodin [artifacts]
2. Kamigawa [tribal]
3. Ravnica [multicolored]
4. Time Spiral [mechanics]
5. Lorwyn [tribal]
6. Shadowmoor [multicolored]
7. Alara [multicolored]
8. Zendikar [tribal]
9. Scars of Mirrodin [artifacts]
10. Innistrad [tribal]
11. Return to Ravnica [multicolored]
The cubes that I think will be the most fun are:
1 and 9. Mirrodin/Scars of Mirrodin: an artifact cube. Who wouldn't want that? It is no surprise that this is the first cube I have attempted and completed. All others are works in progress or not started. I can add to all from the many Innistrad and Return to Ravnica cards I have from opening packs I buy at my local Target.
2 and 7. Kamigawa and Shards of Alara: a Commander cube with the least popular block yet the one with the most legendary creatures (Kamigawa) and one of the most popular blocks also with many legendary creatures, and in the latter case, some of the most popular commanders (Shards of Alara).
3 and 6. Ravnica/Shadowmoor: a multicolored cube with two of the most popular blocks is a no-brainer. Enough said.
4. Time Spiral: this block is all about nostalgia for the mechanics (manifested as abilities) of previous sets. Therefore the best match is with the core set and with pre-Modern sets. This cube may need a small number of cards from all other blocks that are representative of specific abilities. Maybe this is where I can put all those infect cards from the Scars of Mirrodin block that I did not include in the artifacts cube.
5 and 10. Lorwyn and Innistrad: a tribal cube with two of the most popular blocks is yet another no-brainer.
8 and 11. Zendikar and Return to Ravnica: two words-Dual Lands. Yes, Zendikar has the fetch lands and Return to Ravnica has the shock lands. Seems like a match made in dual land heaven. Of course, there are also all those Guild Gates for your casual deck building pleasure!
And then there are the pairings that fit the cards I have. In addition to the Mirrodin/Scars of Mirrodin pairing, the subject of my artifact cube, I also have a veritable mountain of Innistrad block cards, some ready to pair up with Kamigawa, and there is also pairing up Ravnica with Return to Ravnica.
August 20, 2013 edit:
Now that I have a bunch of M10 cards I am thinking of the following super cubes:
1. Tenth Edition + Ravnica + Return to Ravnica [all about the Ravnica guilds]
2. M11 + M12 + Mirrodin + Scars of Mirrodin [all about artifacts with Titans added "to taste"]
3. Lorwyn + Kamigawa + Innistrad [all about tribal]
Time Spiral belongs in a cube with the Legacy cards for which all those mechanics were brought back.
