We've traveled extensively with our tot on our laps with no problems, and we hands down prefer the aisles that have only two seats. The window seat seems to give us more arm support for a sleeping baby. We also try to get the first row in coach, so no one is in front. We'd hate it if our child's occasional playful kicking were to disturb the passengers in front of us.
We also bring new toys that our child has never seen before. This keeps her happily busy during the flight.
Finally, we always "run her ragged" between flights.
Good Luck!