There are two lines, but the second comes from the carbon canister. I'll have to go outside and check mine. I'm pretty sure that's where the line to the purge solenoid hooks up...

EDIT: Alright, I went and looked at mine and I see what you are talking about now. That port is plugged on mine. The line to the purge solenoid is "around the corner" from there. I couldn't find anything in the '00-'02 FSM, so I went to a different source and found a diagram specifically for the 2000 Neon. They were a bit different when it came to emissions. The diagram for the 2000 shows two lines coming off of the throttle body. One to the purge solenoid and the second to the back of the valve cover. On [at least] the 2003+ where that port is plugged, the line goes from the back of the valve cover to the makeup air filter on the airbox itself. See if you have an open port of the back of your valve cover...

 

If that hose is connected from the valve cover to the air box, it's the PCV breather hose.

You can just cover that port on the air box.
Be nice to the environment, and put that hose back in.

Someone unplugged it, and forgot to plug it in after that.

Check the "howto" book to see if I'm correct.

 

Well, no. The PCV valve is on the side of the valve cover and connects to the intake manifold. The picture the OP posted is a port on the throttle body.

 

I know it's connected to the intake manifold but there is another hose called breather hose that is usually goes into the air box, or has its own air filter.

If that port is on the throttle, could it be the ERG vacuum hose?
I don't know any other hose that is connected to the throttle body.

I better not guessing what hose it is. Maybe someone else know.

 

Correct. That line comes from a port on the back of the valve cover. The PCV valve is on the side of it.

The two different diagrams are not available online (that I can find anyways). I'll post the two different ones up later so you can see what I am talking about.

 

 

My 2000 matches the '03+ diagram. I have a "make-up air tube" going from what used to be my air cleaner, to the back of the valve cover, which is referred to as the "PCV filter" in my haynes manual. However, I still have the old port on my throttle body. THat's what I was talking about(the TSB). There was a flaw with the PCV system (not the brake booster) and so they re-routed the make up hose to the air cleaner, and just plugged the old hose port with a little rubber piece that degrades over time and eventually falls off.

 

Ah, OK. Now the re-routing part makes sense. I wasn't sure where it was getting re-routed to exactly (never remembered to check for that TSB either). Sounds like a vacuum cap is all that's needed?

 

Yes I believe that there was just a cap there and it has fallen off. I have both of the lines present that is shown on the pic you post. That is the same diagram which is under the hood of my 2000. I have both lines one to the purge canister which is as you state "around the corner" and then the make up which is plugged in on the airbox itself on the upper left corner if you were looking at it from the throttle body side. This line also has a small filter for it which is in the airbox as well located in a plastic housing. I have temporarily taped over the vacant port and the car runs well. Although it did before too. I will run it this week and cap it permanently this weekend. Thanks for all the help!

 

I think reason they unplugged that hose from the port is because they were afraid the blow by gas from the crank case could freeze up in the throttle body (in the winter), and make the throttle valve stuck.

My goes into the air box cleaner.