Here is a picture of an uncovered nipple. After I did my throttle body, I tried to plug this nipple, but the car would not run like that. There is a vacuum when I touch it. The strange thing is that I tried plugging it today and it runs just fine. I don't know what has changed, but works for me. I assume it was an intake leak when it was not plugged.

 

The nipple for cruise control, if so equipped. IF not, it has a small rubber cap similar to that beside it that should be there. The one beside it is for cars with auto trannies for the kickdown mechanism. You need this to be plugged. Your car will have a high erratic idle and be prone to die sometimes if not(or should anyway). Maybe the reason it would not run with it plugged is because someone didnt know it was open, but the car would not run right so they changed the idle, and now when you recapped it the idle was too low. Definitely cap it and then reset your idle.