Anime

Wotaku - a HUGE list of Streaming/Downloading sites and apps categorized in Languages, Sub/Dubs and more.
The Anime Index - a list of Tools, Apps and Sites for your Anime needs.

Downloading

Nyaa (Torrent) - The Best Public Tracker to get Anime from.
Sukebei (Torrent) - The Best Public Tracker to get Hentai from.
Use Japanese titles to get better results.

The Anime Index (DDL / Torrent) - This site also has Download sites/apps for Anime/Hentai/Manga and more.

AnimeTosho (Torrent) - Collates Releases from Public Trackers, and has DDL links for file attachments (Subtitles, Fonts, Chapters, Tags).

AniDex (Torrent) - Alternative Tracker to get Anime from, A Few Releasers post exclusively here.

AniRena (Torrent) - General Tracker for everything Japanese.

Tokyo Toshokan (Torrent) - A Library for every type of Japanese Media, shared with Torrents.

Nibl Bots | AniMK (XDCC) - Sites indexing IRC Bots where you can Download from using IRC Clients.
Check the AnimePiracy Wiki for a detailed guide into XDCC.

Release Indexes

SeaDex - A big list of the best Releases for Anime organised by Seadex.

A Certain Fansubber's Index - Another list of the top Quality Releases for Anime.

qBittorrent | Deluge | Transmission - Free, Lightweight and open source Torrent Clients.
We do not recommend using uTorrent or BitTorrent, as it came bundled with Adware, Spyware, and Crypto-Miners in the past ^[1]. In its current state, it's Adware and Bloatware. We don't recommend using uTorrent v2.2.1 either due to confirmed Security Exploits.
qBittorrent Enhanced Edition - A qBittorrent fork with enhanced privacy (IP filtering, auto-ban bots and copyright trolls, auto-update public trackers).
qBittorrent Guide - A guide for configuring qBittorrent.

AB-DM | IDM | JD2 | Motrix | FDM - Download Managers that can boost Download speeds. Motrix and FDM support Torrenting, and JD2 is best for downloading multiple files simultaneously. IDM is paid.
Elephant - Adds YT-DLP support to FDM, meaning it can download from all these sites.
JDownloader 2 Guide - A guide for setting up JDownloader 2.

YT-DLP - Can download from over 1500 sites including: Crunchyroll, Funimation, SoundCloud, Bandcamp, PornHub and more. Here's all the supported sites.
Maintained fork of the popular YouTube Downloader youtube-dl with more functionality.
Stacher - A modern YouTube Downloader, front-end/GUI for yt-dlp.
cobalt | community instances - Downloader that supports Instagram, Reddit, TikTok and more.

Taiga (Windows) | Trackma (Linux) - Automatically detects the Anime Videos you watch on your PC and synchronizes your progress with AniList, Kitsu, MyAnimeList and more.
A must have for Weebs.

Misc

The AnimePiracy Wiki - Comprehensive information about everything Anime Piracy. A MUST READ if you are interested.

AnimeThemes | Themes.moe - A huge collection of Ending/Opening Themes for Anime.

SauceNAO | Anime Scene Search Engine - Reverse image search engines for Anime, SauceNAO is also helpful in identifying sauce.

Senpai.moe - Calender for upcoming Official Anime Releases.