Surprised no one mentioned several issues with the aisle seats:

1. The flight attendant opening soda cans and spritzing the nearby aisle inhabitants
2. Passengers boarding with various carryons that bash you going down the aisle. Worst case is the backpack that smashes you in the face when the passenger turns in the aisle to look at space in the opposing overhead. Unless you count the time the passenger bend over to get something off the floor across from you, sticking large _____ in your face.
3. Passengers dropping stuff out of the overhead above you.
4. Passengers using your seat as a hand hold to pull themselves forward, then releasing it suddenly to launch you.

Mrs. Blue47 puts up with this so that she can easily use the lav. Not me.

I recently sat in a middle seat as part of a standby situation.

I now remember why I don't like sitting in the middle unless my wife is next to me.

Window>Aisle>Middle.

I'm unfortunately a lowly silver with Asiana so I never get exit row or bulkhead but I get to lean against the wall if I ever feel like dozing off (I can never get any kind of deep REM sleep on airplanes) and I'm lazy so getting up for people is obviously a pain in the butt. The only time I ever use the bathroom on airplanes is if I'm flying a foreign carrier. US carriers' bathrooms are disgusting. I'm always scared that I'll catch something if I go in there.

When you're on the window, the wall curves inwards, taking away valuable foot and leg space if you have longer legs.

I have to say I've always preferred the window. Ever since my first flight as a child (sooooo long ago), I've had my nose pressed against that window from taxi out to arrival many times. I love to watch the scenery go by.

When it's a long flight or overnight flight, I sleep better in a window seat as I can lean against the wall.

Also, I usually don't have to get up that often, so I don't have to bother the person in the aisle or middle.

The window. If its daylight you can look outside. If its dark or you are tired you can sleep without being awaken by your seatmate.
BW

I prefer aisle seat because it is easier for me to get up for restroom or walk around to stretch.

Window, short flights I just bunk up and relax, watch TV, etc. Long flights I SLEEP. I like being able to just relax and not worry about others having to get up during the flight and making me get up too. I don't get up out of my seat on any flight less than 4 hours on average.

Short flights - aisle always.

Nighttime, window. Scenic Areas (Grand Canyon, NYC, etc), window.

Long flights - prefer aisle.

What is interesting (perhaps odd is a better word) :D - is when Mr Sophie and I travel together. He is 6'5 and I am 5'8". When we fly together and cannot get exit, bulkhead, or 1st, I take the aisle in front of him so that he does not have to deal with someone laying their seat back. If we CAN get exit or bulkhead, then we sit cross aisles, as we both hate the middle.

window, always (better view and I don't get bumped by people in the aisle)

aisle for me
 

being the orthopedic shoe 'n orthotic ter'wrist that i am ;), i need to occasionally get up and walk when my surgically repaired ankle "reminds me" and i don't want to disturb my seat mate (and for those that fly united, i will pass on an e+ middle or window and take an e- aisle for the same reason)

It all depends on circumstance. If flying solo I'll go for the aisle, I can get up and walk around more easily and to be honest if I really want the view I'll had down to an exit area for a look. If travelling with others, I'll try for a pair of seats down the back of a 744 and take the window with the bonus legroom that you get at the side of some of those seats.

For First or Business Class it depends on the airline. But for economy definately aisle.

Window for the most part.

Hi

I prefer aisle on long haul. It makes it a lot easier getting up and walking around to stretch the legs :-)