Lets say that my home has 2 bedrooms, 2.5 bathrooms, laundry, kitchen, Office, and a workroom(I like to tinker). So we are going to need six room controllers. So we will need several sensors in each of the rooms which in turn feed in the corresponding room controller. For starters, we will need to measure the temperature and humidity. This can be handled by a DHT22 this is a serial device which simplifies integration.
We need a way to talk to the user so we need some sort of display, and a few buttons to boot. each 'thermostat' talks to the room or area controller. So we need some sort of communications between the two devices, and the 'thermostat' needs a little smarts, why don't we use some sort of Arduino. For Prototyping I will use a Mega R3 but down the road I will most likely do my own small factor copper board. But on second thought I could use a TI MSP430 with K350QVG-S1 Kentec QVGA Display BoosterPack that has a 320 x 240 pixel display which is a touch screen as well.
Also in each room there are fire/smoke detectors, which also connect to the room controller. In case of fire, the room controller shuts off the vents to/from the room, as not to feed the fire with fresh air, or to blow smoke through out the habitat.
Last but not least is the question of how air is getting past the filters? Answer: Two Mass-Flow Sensor just like your car but a bit smaller .
Just a quick note you could also include a Honeywell Air Quality Sensor HPMA1150SO there kind of cool and they only cost about 40 bucks, they are a serial device so they are no brainer to install or code. If you are going to install this you also might install a Radon Gas detector a well. Even though these devices are not room related but more whole hab sensors I decided to include them here as well.