I've limited myself to seven shelves of books, any more than that and I cull the lot.
I've not got much of system, but it works for me.
Three are in my family room.
One shelf is solely for fiction.
One deals with interpretation, this shelf also contains various hermeneutical approaches to the science and Genesis debates.
The last contains translations by individuals, (e.g. Alter, Fox), books on interpretation and structure of OT narrative as well as books dealing with biblical authority, inerrancy and a bit of interpretation.
In my 'library' I have four full shelves.
One is for the physical sciences and history.
Another contains concordances, lexicons, dictionaries, and Hebrew and Greek grammars, with a smattering of other related material.
Next to it is a full shelf of commentaries arranged by biblical book.
I've got half a book case for doctrine and Systematic Theology texts. Under these are two shelves of various translations and old bibles.
The bottom (taller) shelves of each bookcase contains notebooks of articles, notes and class material I felt was worth keeping.
Lastly there's my bedside shelf where I keep books I read, want to read, or have read and want to read again and again. Arranged haphazardly.
The number of books is small enough that I know where every book is without much though.
Many of the books I've purchased recently have been digital.
Rob