Love this question; curious how other folks do it too!
I try to keep Goodreads up to date for organizing what I have read and want to read. I used to have a really intense “shelf” system going on Goodreads but one day I decided it wasn’t helpful and deleted all of my shelves except for “read” and “want to read” and “queued up.” I kind of regret this impulsive deletion - I had this one shelf called “Slim Volumes by Women” (e.g. Women by Chloe Caldwell, Bluets by Maggie Nelson, The Self Unstable by Elissa Gabbert, Dept. of Speculation by Jenny Ofill etc) that I often find myself wanting to link people to before I remember that I deleted it.
I have tried to use Are.na for organizing my books, but for some reason it hasn’t clicked for me. So I continue using Goodreads, sort of by force of habit. I’d love to use something else, though, in an attempt to engage with Amazon as little as possible. It felt ironic/bad to use Goodreads to give five stars to Seasonal Associate by Heike Geissler, a book about the misery of working in an Amazon fulfillment center.
For my physical books, I used to not pay any attention to how they were arranged but then in college I read something in one of Susan Sontag’s diaries about how you can judge the seriousness of a person by how their books are arranged. This is obviously untrue, but at the time I was like “Oh no, if I wanna be ‘serious’ I better think about how I arrange my books.” So the system I devised then has persisted to the present day, with little reflection or refinement:
I have my shelves sorted into fiction, standard non-fiction, non-fiction about design, and self-help-y non-fiction (which I hide in a bottom corner of my office in the hopes no one will judge how much my self needs to be helped based on the quantity of books there ) . And then within those categories they are alphabetical by author. It makes it easier to find things I’m looking for and sometimes the collisions of authors beside each other makes me laugh, but besides that I don’t think it is necessarily that great of a system.
I googled around to try to find the Sontag quote about seriousness and organization. Couldn’t find it, but I did come across this write up of how 11 writers organize their books; kind of interesting: https://lithub.com/how-11-writers-organize-their-personal-libraries/