Most efficient Big Reactor and how to automate it?

To calculate the efficiency of a reactor you can use the BigReactor Simulator at http://br.sidoh.org/

I always start with a 3x3x3 reactor. Inside I place five fuel rods. For cooling I use "Gelid Cryotheum". Here you can see this configuration. I don't know if that is a good idea or not but I think it produces enough energy to power your machines.

Later you might want to power a turbine with your reactor. You need to provide water to the reactor which is used to make steam and power the turbine. You can place the turbine on top of the reactor. I often use a 5x5x10 turbine with my 5x5x5 reactor. As far as I've seen that's pretty much the best turbine size in combination with that reactor.

I think it is also possible to automate your reactor and turbine if you want to. ComputerCraft is the way to go. Unluckily I don't know a lot about that mod. I just found this helpful page on the computercraft forum. I hope this helps.

Mabu's answer is correct, but I have a very simple way to automate the reactor to only produce as much energy as you are using. It will never waste energy.

First put two redstone ports in your reactor. Set on of them to trigger when your reactor's internal buffer is below 50%, and set the other one to turn the reactor on. Then connect them with redstone. Voila! It's automated.