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I am curious why you asked about alternatives instead of Zotero if it's your first time seeing it. Zotero is simple and extremely popular. With third-party extensions, it has enhanced capabilities. It has a PDF viewer and you can annotate the files. Finally, there is an iPad app that works very well.

Edit: A very popular thread from just 8 months ago - https://news.ycombinator.com/item?id=30714121

Jabref, which use .bib file as storage. The importing features are almost the same (all major sources supported). Tagging and note taking are nice. Full text search is implemented with the mighty lucene. Word plugin and Browser import plugin are good too.

Both zotero and jabref are on similar level of simplicity. However, they are very different on details if you use them heavily.

All the alternatives are shit. Zotero is the open source pinnacle for reference managers.

Not only that, but Zotero are also incredibly generous with their storage offer. You can read and annotate PDFs on your iPad and have the annotations sync instantly with the desktop client. You can then import the annotations into Obsidian for post-processing and create flashcards, which you can then sync with Anki.