Note: some mirrors of the pages linked below may not work. Please lmk if there are dead mirrors!
R74n: I used to go on this site. Contains some very useful tools and games and pixel art. Too bad it's full of Google ads now. (GitHub page)
Tenebris (TOR Only!): a forum on the dark web. Contains some really useful programming and hacking threads.
Spyware Watchdog (TOR) (I2P) (Freenet) (Zeronet): very useful if you want to check software for spyware. (Git Repo)
Shadow Wiki (TOR) (I2P): Largely inspired me on making my blog. Contains some very nice tips about anonymity, and gives advice on browsers, email providers etc.
Diyar Ciftci (Clearnet) (TOR) (I2P): Another blogger I have read. Also includes some good articles about privacy and anonymity. Also includes some useful tools (such as a link shortener).
Richard Stallman: A director of the Free Software Foundation and the Chief GNUisaince of the GNU Project.