best practices for organizing digital and physical articles
I have them organized similarly to the blog post you linked. I'm not sure it is the optimal way, but it works quite well.


The central search key for me is (First)AuthorYEAR. By now I know my way around in my field so that the author names are meaningful. And easier to remember exactly than title abbreviations. 
I try to have almost all papers also digitally, and organize them with jabref. I started using jabref before Mendeley, Zotero &amp; Co came up and didn't change.  
jabref allows to assign the papers to topics/groups, which can be hierarchically organized, but a paper can also belong to several of them.
This is important for me, because one paper may be about an application (e.g. tumor diagnostics -> group with tumour or cell type), use specific measurement technique (group that), and maybe use or invent an interesting data analysis technique (group there). 
Jabref stores its information in a .bib file (with a few non-standard fields and some more info in comments at the end). But essentially I can work with this file as with any other .bib file.
.bib and digital versions are in a git repo which basically solved the mess of having lots of copies that go out of sync while I'm still able to work completely offline. As .bib is a text format, version control works fine with that. Papers usually do not change, so it doesn't really matter for the version control that they are binary data.
When looking for a paper, I usually search for it in jabref, and then look whether I do have a printed copy (I'm too lazy to keep track of printed status).
physical copies I keep in two drawers with a suspension filing system. One has collections of important papers on topics I'm interested in. The other keeps other physical copies alphabetically by author name (one folder for each letter so far, some will be split soon). 
I tried before with normal lever arch files, but was too lazy to put papers away into their proper place. 
For a while I had the luxury of working with dual monitors. During that time I printed considerably less papers. Now I have to work with only a single (and not too big) monitor again, and again print most papers.