There are many different plane configurations: 3&3 (737, 757, Airbus), 2&3 (MD-80), 2&2 (CRJ and some ERJ) and 2&1 (ERJ), so it would depend on what airline you are flying and on what type of plane, to an extent. If you're flying SWA, you won't even have seat assignments and will have to deal with it all when you board.
An MD-80, which American still flies a lot of, would be perfect, IMO, since a row is five seats across. With five in an 3&3 configuration, I'd do three on one side of the aisle and the aisle/middle on the other. I just don't want to deal with even the minor hassle of negotiating a seat switch if someone does get the middle seat. And I'd advise you not to try the middle seat trick when boarding a full or mostly full Southwest flight.
The back of the plane, on MD-80s especially, is my least favorite place to be. It can be very noisy (MD-80 engines are back there, not under the wings) and it takes forever to get off of the plane. On the other hand, it does tend to fill up last and you may have a better chance of getting an empty middle seat back there. The one thing to consider about the middle of the plane is that children can't be seated in exit rows, which generally are over the wings. A final consideration is if you want a power source for a DVD player, computer, etc. they tend to be more prevalent in the front of the plane and get fewer and further between the more you move toward the back. Some planes don't even have them at all, so this point may be moot in your case.
A great resource to look at all the aspects of seating is
www.seatguru.com.. Pick your airline and the plane you're flying and they give your great info.