You ask a good question Grasshopper... It's all about the airplane itself, then about the upgrade, whether you want to work or rest, how quickly you want to get off the plane when it lands, and, of course, the length of flight.
For example, on the Airbus A319, if I'm upgraded and plan to work, the best seat is 1B (decent legroom, no one to lean back into your workspace). If I want to rest, better to be in row 2 (more legroom, but it can have more limited recline, especially in the winter when winter coats are hanging behind the seats) and at the window (not disturbed by someone else getting up). On the Airbus A320, if you are upgraded and you want to rest, the best seats will be in row 2 (more legroom, uninhibited recline) and, if you have a large bladder, window (2A or 2D). Row 3 has the recline limit issue. Row 1 has the legroom issue.
Right side vs Left side only comes into play in wide-body aircraft and is mostly about getting off the airplane first. (Of course, you first have to figure out which is right and which is left (the right side of the plane is the side with the higher seat letters (the side on the right when you are sitting in your seat)). On wide-body such as the Boeing 777 (Triple-7 for us in the industry :-)), The left side in Business or First Class will typically empty a bit faster than the right, but in Coach, it seems to be the opposite (not that I get much experience back there :-)).
Of course, the best seat you can have in business class (on United at least) is the upstairs window seat on the Boeing 747 (towards the rear, like row 17 or 18, again because of that fast exit policy -- although you are clearly giving up some exit priority by being upstairs).
I could go on and on and on, but you get the picture.
A lesser person, of course, falls back to using the best web source for seating information: Seat Guru -- they're OK, but not as useful as real-world experience.