On the factory intake piping, there are these tubes that go off into empty plastic reservoirs. There is a big one before the air filter and a smaller one after the air filter. What is the purpose of these?

They are resonators. They make the car quieter.

Yep, you can remove both of them if you want. The one that is after the MAF can be easily plugged off if you take the hose off and fit in an appropriately sized PCV pipe endcap.

Aaron

Originally posted by luminus
The one that is after the MAF can be easily plugged off if you take the hose off and fit in an appropriately sized PCV pipe endcap.

I've heard that a Gatorade cap or a Mobil1 cap fits nicely on there too. I personally stuffed a golf ball in there. Gets a good reaction when I go through tech at autocrosses. :D