Chris,
the one at the side of the engine head is the main temp sensor that is most likely attached to your gauge.
The one in the thermostat housing is a sensor too, but may be part of the emissions system.
Both parts with the rubber boots are emissions switches. They open or close, allowing vacuum to be utilized in the control of emissions. Since they are capped off, they are not active and can be removed and plugged, unless the government requires emissions systems be working.