For the past few months my beetle will shut off after warming up to operating temperature in between shifts, while in neutral, and with the clutch pressed in. Anyone have any thoughts as to why this is happening?

 

Hmm, I will suggest you to check out the coolant level and perhaps it is the time to flush the radiator, because most of such kind of heating up problem and sudden shut down occurs just because of these two factors.

 

What year is your car? Does it have a CEL (Check Engine Light)?

My experience is that cam sensors usually cause those random issues but that will usually toss a CEL.

Another issue may be a failing fuel pump or fuel pump relay. I have noticed that alost EVERY VW in the junk yard has all of the relays pulled. That leads me to believe VW's have issues with relays all the time.

Does the car start right back up and drive? If so, likely a fuel related issue.