During my sophomore year in college, I got into trouble with the honor code. I ended up with an F in the class and a permanent note in my student files.

 It was one of the biggest mistakes of my life, and I regret it to this day. If I could change one thing about my life, it would be this incident.

Now, over three years later, I'm looking to get a job. Will this sort of thing come up during a background check? There was no transcript notation, and from what I understand, student records are confidential information.

 What sort of effect would this have on my ability to get a good job?

Feel free to send me a private message.

It might depending on how deeply each employer goes and often that is dependent on the actual job. Some just check to see if you actually got the degree that you are claiming. Some might ask for a transcript.  While there is only a small possibility that it will be found out, this big huge world can be a really small place, especially in some industries.  You never know who knows who. 

And I have my doubts that student records are considered "confidential information", just like (most) employment records aren't although some companies have a policy to keep them as confidential as possible.