Obsidian: build your own wiki with Markdown; supports Interpage link and link-tracking as well as advanced search and file attachments; also has built-in file manager and PDF viewer.
Foxit Reader: my favorite PDF reader. Fast, lightweight, and free; equipped with advanced search functions (e.g. folder search and search & highlight) and split view (so you can read two parts of the document at once, such as main text and end notes). For OCR and other advanced features, it costs only $5 per year for students & educators.
Xodo PDF: touchscreen friendly, smooth operation, and also free; supports page manipulations (rotation, rearranging, deletion, etc.) but a bit more unstable than Adobe Acrobat or Foxit.
In addition to paid apps such as Adobe Acrobat and Foxit Reader (see above), PDF-XChange Editor is the only easy-to-use and reliable free OCR app that I can find.
Split View in Foxit Reader