Window or Aisle?
The window-aisle civil war continues.
If your flight is mostly in daylight and the kids are old enough to enjoy it, the window is great fun. If your kids (or maybe you) need to use the toilet a lot, get the aisle, as after 14 hours into a 16 hour you will run out of things to say to the person on the aisle you are crawling over for the 700th time.
A really cool book for frequently flying kids or just the curious is Window Seat: Reading the Landscape from the Air. Basically, it explains what it is you're seeing when you're up in the air.
If you are indeed the person who sat in the aisle on our last trip, I am sorry. Carry a copy of this with you next time, or maybe ask us to exchange seats with you.
Young children should not sit in an aisle seat. The carts used for meals service take up almost the whole aisle, and a little one's dangling arm could get clipped.
Another great undecided issue is the best configuration for traveling with kids. This depends somewhat on how the seats are arranged, but here is our advice.