The Programmer's Journal
More often called a “lab notebook” or “inventor’s journal” (or notebook, etc). In the process of contributing to a project which would benefit from my use of a programmer’s journal I did a notable amount of research, which I’ll drop here.
Essentially the journal should more or less serve two purposes, to document your project (thoughts, inspiration, ideas, actual work, etc) for your own benefit and to provide a record for copyright purposes (though supposedly this aspect lessens in first-to-file patent systems, instead journals are especially useful in first-to-invent patent systems). This imposes a few requirements. At bare minimum the notebook needs to be able to demonstrate signs of tampering when it occurs, this means no perforated pages or spiral/wire bindings. Additionally pages need to be numbered and dated. Nothing should be erased, only crossed out, and everything should be done in ink. Ideally you should sign each page and eventually it should be inspected by an additional individual who also signs the page (and have some kind of demonstratable understanding of the material).
For ideal pens/inks, I have no idea. But for notebooks I have some options. Vela Workings (out of Grand Rapids, MI) have some nice looking options on Amazon. Scientific Notebook Company seems to have some good options. Similarly BookFactory (out of Ohio and veteran owned) has some nice books. If something less lab-chic and more moleskin-like is your desire most of the Leuchtturm notebooks fulfill the minimum requirements. You can find them in different sizes and styles on Amazon.