I found The Advanced TeXbook by David Salomon to be helpful. It shows how to make your own format on top of plain TeX, including table of contents, page numbering, cross-references and insertions.

I also found A Beginner's Book of TeX by Raymond Seroul and Silvio Levy helpful as a quick reference.

Also I have an anti-recommendation for Knuth's TeXBook. I did not find this book helpful at all- too much information buried in exercises (which I don't think is appropriate for a reference), and not enough directly said on how to do useful things. Figure out how to make a table of contents using only the TeXBook..