In general, upgrades are awarded to the most loyal flyers as determined by frequent flyer mileage. As you build up mileage and thus elite status, the system will "reward" you with upgrade certificates you can redeem on future flights. Therefore, many times it's in your best interest to spend a little more in order to keep all your miles flown on the same airline, or at least in the same alliance partners. Also, if your chosen airline offers a credit card, use it to build up the miles. When a flight is overbooked and they need to make room in economy class, often times they will upgrade the highest-mileage people to make room.
Often times, a number of seats are held by the gate agents to allow for flexibility for seat changes. For example, families who need to sit together or disabled people who need special access to an aisle or near the loo. If it gets closer to departure and they're still open, usually you can have them. Though now that they make you pay for the best seats ("Economy Plus"), it can be more difficult as that's where these seats usually are.
Your seat cushion is designed to come off. The cushions and fabric covers get changed out every so often during overnight maintenance. Also, the seat cushion can be used as a flotation device in the event your flight becomes a cruise.