Window vs. aisle seats is a preference thing. In the aisle, you feel less crammed in and can stick your legs out when people aren't walking by. In the window, you can look out (obviously), and you can lean against the wall (like if you want to sleep or something), which can be nice when you're traveling alone and don't want to sleep on the person next to you...
I prefer the window, but the decision is more of a personal preference.
Some things to think about:
The bulkhead (the very first row of coach) has more leg room.
The emergency exit row has about 3 inches of extra room (so that people could get out of the plane if they had to), so if you like a window but are concerned with leg room, think about that.
Do not book the row in front of the exit row, as those seats do not recline.
Also, on certain planes (when you book the flight it should tell you what kind of plane it is) there are two exit rows together. The first of the two rows only has a middle and an aisle, so the window seat of the second exit row is the best seat in the house.
Don't sit in the very back, as that's where the bathrooms are, so there are always people standing right next to you, the toilets are loud, and every once in a while smells will come out.
Find out what time of plane you will be traveling on, and visit seatexpert.com or seatguru.com.
Also, check out these videos about seats on planes.
http://www.youtube.com/watch?v=UXhy6QZZJbw&NR=1
http://www.youtube.com/watch?v=guvJHKZhUv8