I began thinking about this when I saw a post (via @shareski) on Twitter asking how people had their classrooms arranged. I have had the "opportunity" to arrange 11 classrooms, though I've only been teaching for 6 1/2 years, so I've tried many things. In my first year teaching (6th grade), I started with rows, and then moved on to pairs, and eventually grouped, and then back to rows (it was an...exciting year.) :-) I told them we had to move back to rows because they "couldn't handle" sitting together, in terms of behavior (which was true).
As I was pondering the possibilities for the next school year though, I decided that I was going to think positive and start in groups (which is always my personal preference). I did this, and never changed back. The biggest benefit I saw to groups (in addition to all the supporting research), was that it forced kids to learn how to deal with each other. This sounds a little coercive, but I prefer to call it educating :-) When they thought that there was no other option, they found a way to make it work. Albeit, every year, I had conversations about how it's an important thing to learn with kids who wanted to change seats. (I think the discussion went something like: "You don't have to like them, you just need to be able to work in the same space. This is an important skill that everyone has to learn at work-even teachers--, and it's even better if you learn it now!") This method worked the best for me through the years, particularly because we did lots of group work.
At the end of the 2009-10 school year, I let my 7th graders choose how they wanted the room arranged for the last week or two of school. After a vote, they decided to go with one big circle. While it was a physical nightmare because we couldn't get to anything outside the circle, the kids loved being able to see everyone at once, and it led to some fun discussions.
This year, when I began teaching computers, I had to set up a new style of classroom. Not only that, since I'm a traveling teacher at 4 schools, I had 4 labs to set up! 2 of the labs are laptops and the others are desktops. In the laptop labs, I have round tables with 5-6 laptops apiece, which works fairly well. In my desktop labs, computers are arranged in groups of 6 on tables, which functions in pretty much the same way.
The most important thing when using technology with middle schoolers has been to have them in places where they are next to someone at all times. The logic behind this is that someone always missed where to click, which menu the command is on, or typed .com instead of .org. When they need to verify something, there is always someone to help, which seems to be a more critical element with technology than with regular content teaching. (And it helps save my sanity, so I don't have to answer every easy question!)
No matter what, I'm always in the process of determining who needs to sit in a different combination, but the arrangement in groups always stays the same. :-)