Has the car been converted from automatic to manual at some point? The automatic cars have a vacuum valve controlling the idling speed and it could be that some of these lines were not connected when the car was converted?
Top picture, both pipes should connect to the air filter. The bigger pipe is the crankcase breather and the second pipe is the EGR (exhaust gas recirculation) valve pipe (
I think 
) Has your car been fitted with a K&N (or similar) air filter? A lot of people don't know what to do with these pipes once they change the standard air filter.
The two unconnected pipes on the manifold are meant to connect to water pipes for manifold heating? This is the case with automatic cars but might not be for manuals.