To get back on topic, here are my suggestions for making a long flight more pleasant:
1. Fly business class if you can afford it or if you can upgrade. It makes a huge difference on a long flight. Or chose an airline which offers a choice of paying a bit more for more room in economy, such as United Airlines Economy Plus.
2. Do take off your shoes. Bring lightweight slippers or an old pair of socks to wear during a flight.
3. Aisle seats are good because it's easier to get up and walk around. The cons are you are often bumped by food and beverage carts, people grabbing the back of the seats as they walk down the aisle, and you may have to get up frequently to let out the other people in your row.
4. Try and get exit row seats (if you aren't traveling with children under 14 and are not disabled in any way). These are often reserved for elite frequent flyers, but you can sometimes pay to select these seats. Be careful though, some exit row seats do not recline, such as on United, where rows 20-21 are exit row seats, but row 20 doesn't recline.
5. Choose your flight carefully. Check the plane configuration of your proposed flight at seatguru.com. It will show you the good seats and seats to avoid. Look at the seat map of your flight to see what seats are available for seat selection. Look at the amenities available on your flight; are their electric plugs at each seat, is there individual seat back entertainment or those outdated overhead monitors, or no entertainment at all? Does the plane have those horrible slimline seats? What is the seat pitch? All this information is on seatguru.
I have chosen flights just based on type of plane (prices being equal) when I know one plane has limited seat selection, or has slimline seats, etc.
6. Try and chose a nonstop routing if possible, or the fewest stops you can. Nonstop flights are not always the most expensive, and even if they cost a bit more than taking a direct flight or flight with connections, you will find it well worth it if you're traveling for many hours.
7. For an overnight flight, bring your own lightweight blanket, if you have room in your carry-on. If you are worried about germs items on the plane, it's the blankets and pillows which don't get cleaned frequently.
8. Never depend on the inflight entertainment. I have been on a number of flights where it hasn't worked. I bring a book, my Kindle and my iPad with music, movies and TV shows. A pair of noise canceling headphones are a must. You don't have to spend a fortune; you can find decent pairs for under $100. I also like to bring a small flashlight, such as a Maglight. If your overhead light is broken, it can come in handy.