I use it to 1) store ideas, concepts, etc. in a markdown format. So, if I'm studying something - say backpropagation for neural networks - I create the note, search for material online, study it, and add links, images, formulas, etc. to the note so I can merge several good sources of information that would otherwise be scattered in PDFs, stack overflow, wikipedia, ... Then afterwards I can go back and read my note and maybe visit the links I used to obtain the initial understanding. It's really great so far.

2) I can link the notes to create a sort of personal wikipedia. So far I'm pretty happy with Zettlr for this purpose.

I find that even if I don't have to go back to many notes or actively walk through the graph it's really useful for distilling knowledge.