Question: I am in the process of writing a message queue system.

My question is... Is it better to do this queue with files or in a database?

If I were to choose the database, it needs to check for new jobs every second and that just seems a bit of an overhead to me?

If it's files I guess you just constantly monitor the folder and execute based on that?

BR,

Answer: 
I choose option "C" — use message queue that's already built in to Windows:

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Are you writing a message queue system because you want to write a message queue system; or is this just part of solving a bigger problem?

I would suggest not writing a new message queue system. You can use MSMQ or something else off the shelf.