What skills do self-taught programmers commonly lack? What should a self-taught programmer study to get up to speed with his/her formally-educated peers?

It depends on what the non-self taught person you are comparing against did. I would say there are a ton of differences between a computer science major and a software engineering major. Compared to computer science, you’re programming skills will be lacking (just due to time doing it, consider that they program every day all day for 4 years straight). But bigger than that is that you won’t understand how anything works. Maybe you can open a file and read and write, but do you have any clue how the programming language made that happen via communicating with the OS? Comp sci people do. They know how the compiler works. They know how to write in a compiled language (a lot of self-taught people have never done that???). A lot of answers talk about design patterns and junk. I still don’t know any of that after getting a comp sci degree and working for 15 years. They are probably comparing to what you learn in software engineering.