Motorcycles

I prefer side because they keep the weight lower and allow me to more easily swing a leg over.
When I tour I need extra space, so I end up with both.

I love my panniers on the Z1000SX/Ninja 1000, they integrate seamlessly into the rear handles so you can't tell the bike can carry bags unless they're on. They can fit a helmet and they look nice. Starter key of course also opens the bags and locks them to the bike.

I had a top box on an older Honda, terrible experience. Taking the bag off the bike meant working with the same mechanism that held the bag shut. One time going to a date of course resulted in opening the bag while taking it off and spilling the contents in front of her.

I've been riding a big bike (mts1200) and I prefer the side bags. They provide some protection from me dropping it, they lower the centre of gravity a little bit, and they can technically hold more in them.

Using the top box would make me more top heavy than I already am.

I wish I could fit my helmet in the panniers, but its the price I must pay.