I was looking at an engine from the mazda 626, and it had one main throttle body plate and two other ones(side by side) behind it that opened up. What does this do for the engine?

 

Sounds like a variable intake runner system. The idea is that at low engine speeds, the longer runner is used to create intake charge velocity, which helps torque. At higher RPMs, it's better to have shorter runners to prevent too much resistance from building up. This phenomenon is one of the reasons that N/A motors almost always have relatively narrow power bands (if they make decent power, anyway). Essentially it's why an N/A motor has peak torque at one specific point. Intake and exhaust manifold length, along with port diameter and cam profile, are what determines this for the most part. This also applies to exhaust manifolds, though to a lesser extent and for different reasons.

And those factors are why Subaru motors always feel stronger in the mid range than other 4 cylinder motors but don't make the high end power like an inline 4. Boxer motors (at least the ones with a single throttle body and a 4-into-1 exhaust) have longer runners than any other 4 cylinder engine design in mass production.

 

Wow, thats awesome, and by runner I 'm guessing that you are refering to the distance between the throttle body and the intake port? Thanks for the reply, that is EXACTLY what I wanted to know .

 

If you look at intake on RX8 (called Sequential Dynamic Intake System), it gets even crazier.
It's got like 5 electric valves in the intake aside from electric throttle body and changes the flow of intake as the rpm shifts.

The valiable intake technology has been around quite a long time, you can even see it in AE86's 4AG

The characteristics of Boxer motor comes from the short stroke, big bore configuration as well.