I've been on somewhere around 70 planes of all different shapes and sizes just this year and there's no perfect answer to the question. My preference depends on the type of plane, the make up of my party, etc. Other than noise, I've never noticed much difference in the "ride" from seat to seat.
On an MD-80, for example, you have two seats on one side of the aisle and three on the other. Also, the engines are in the back so the seats in the last couple of rows can be very loud. With a party of two or a party of four, I prefer two consecutive rows in the two side. Everybody then gets a window or aisle seat. Rows 20 and 21 are exit row seats, so you get a bunch more leg room, which is nice, but those seats are usually reserved for frequent fliers and you can't sit there with kids. Also, with kids I prefer to sit farther up front so you can get off of the plane faster.
A 757, on the other hand, has three seats on each side of the aisle, which calls for a different strategy. Also, the engines are under the wings so the back isn't as loud. Other planes may board in the center of the cabin, instead of the front, so the easy on and off rows are likely to be different.
My advice, therefore, is know the specific equipment you're flying and what the most important things are for you, then determine where is the best place to sit. Unfortunately, your options are sometimes very limited so it doesn't really matter.