I like LogSeq and Zettelkasten for notes.
I keep track of my library with LibraryCat and LibraryThing
I organize news articles, journals, and other web or PDF documents with Zotero. Extra storage has gotten expensive and am in the process of migrating to a self-hosted data server
I use YaCy to track sites on topics I care about, including all of my PDF books, studies, and other writings.