A cruise ship is not like a hotel. In hotels, the rooms can be interchangeable. On a cruise ship, the exact location of the room can make a huge difference.
Probably the first thing that most cruisers look at is the square footage of the room. You aren't spending a lot of time in your room - but you are spending SOME time. The room is going to be small. But sometimes it's worth it to pay a little extra and gain that space to move around. This is especially true if you have more than 2 people in that room.
Lower Floor = Less Motion
A ship is like a tree. The lower part is relatively stationary, being held in the water. The upper part moves from side to side with the waves and wind. The higher up you are, the more motion you are likely to get. This of course can be affected by the size of the ship and by the weather you are moving through.
Lower Floor = Longer Elevator Waits
The lower you are in the depths of the ship, the further you are from where all the action is - the restaurants, shows, casino, pools. There are a LOT of people on the ship and they all tend to like the elevators :) So if you're up high, you usually have an easy time with elevators and can always walk if you wish. If you're down deep, then you have quite a hike ahead of you if you want to go back and forth to your room.
Port - Starboard Sides of the Ship
When a ship moves from location to location, there is typically a side of the ship with a view of the land, and a side that just looks out at the ocean. By mapping out the ship's course, you can determine which side of the ship will give you the most views. This of course assumes that you have a window :)
Near the Engines
Engines of course power the ship, and tend to rumble as they do so. This creates vibration and noise. Depending on the ship, being close to the engines can not only cause those two issues, but also an aroma as well. That's why the rooms in this area tend to be cheaper.
Near the Jogging Track
Some ships promote being on the Promenade level as being a wonderful boon. But typically these rooms have their windows looking right out on the jogging track. People will be walking, jogging, laughing and yelling right outside your room at all hours of the day and night. If you're a party animal, this might be perfect for you. If you're a family with young kids, it might not be as thrilling.
In general, the higher you are on the ship, the more you tend to pay - and also the nicer the room is. The exact same size room might have much nicer decor and view because it is up higher. It is also more convenient to all amenities on the ship. So it's a trade-off that each cruise passenger must make, deciding how much money they wish to spend in return for how much ease of use.