Ok, I think a few things need cleared up about transmissions and gears, because it seems that a lot of you don't understand. The idea of a gear train is to trade of speed for torque or vise versa. Gear something down you can get more torque, but you lose speed. When it comes to motors/engines gears help to convert the engines speed from 6000 rpm and 300 lb*ft of torque to something more useful for propeling a car. 300 lb*ft of torque is not enough to make a 3500 lbs car accelerate at any usuable rate. Also, if you turned the rear wheels at 6000 rpm you would be doing 40,841 ft per minute (6.8 ft per rev) or 7.73 miles per minute (5,280 ft per mile) which is 464 mph. So, first gear in a trans is to trade off speed for torque. OD is basically used to trade off torque for speed.
When it comes to the number of gears in a trans the number of gears and the actual ratios that are picked depend on the application. If 1st gear can give you a lot of off the line acceleration and OD can give you top speed, then you can use gears in between to give you different levels of acceleration or speed to bridge the gap. Every time that you use a gear there is some range that the engine's rpm is going to overlap into the range of the next gear's. 6000 rpm in 1st is, for instance, 1000 rpm in OD. The more gears that you add the more each gear's rpm range overlaps the next gear's. The idea is to select the number of gears and their ratio so that the gear's rpm bands overlap so that the engine is always in its power band. For example, the 4.6L like to make its most power in n/a "stockish" form from 3500 to 5500 rpm. You want to select the number of gears and their ratios so that through your whole race that you can always select a gear to stay in this rpm range to maximize performance. Less gears mean that you will have to go out of the engine's power band. The trade off of having more gears is that you have to shift more often. The closer the rpm ranges the more peak power you can uses.
Averaging the power of the gears is the baest way to see this. With only 3 spds you power usage would look like 3 peaks overlapped where there is a large space between the peaks. As you added more gears the peaks become closer together, and the average power used goes up. See picture.
The engine's power band has a lot to do with how many gears you have. Engine's with "peaky" power bands require trans with more gears to keep the car inteh power band. Themore power you make through out the rpm band the less important the number of gears that you have. Yes, I know the new cobra comes with a 6 speed. That is however due to the fact that the car is designed for road racing where being in the peak of teh power band is very important. Also, I think a lot of it has to do with the "coolness" factor.
The rear end gear basically scales all the ratios up and down by the same amount, and is used to give you more overall top speed or more off the line accel.