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Torrent Trackers & Search Engines
I've listed both public and private torrent trackers that I use and enjoy though its getting harder to find good public sites. More and more are moving to signup only, indicated here by a 
. Some private sites are impossible to find a slot in, you won't find those here. In the list are a number of niche trackers so you can find a link to a quality site with files covering a specific area of interest. Questions about BitTorrent? Visit the BitTorrent Info page for more information.
General (Index multiple torrent types from movies to music to books)
BitSoup - A private tracker that has long been a favorite with many downloaders. Recently there have been accusations of "draconian" forum moderation and tough administration though my personal experience has been generally good.
btjunkie - Searches both public and private trackers and is the world's largest torrent index.
H33T - Focuses on quality descriptions for uploaded files
ClearBits - Since 2003, formerly know as LegalTorrents, they have hosted and distributed open licensed (Creative Commons) digital media.
Seedpeer - Site created from the merging of Meganova and various other sites known for its simplestic design and massively large database.
SUMO Torrent - Started in March 2007 as an alternative to existing sites that were full of advestisements. Endeavors to provide a simple to use search interface with a steady stream of new features.
The Pirate Bay - Once the premiere torrent destination, everything changed in April 2009 when the four founding memebers were sentenced to a year in jail and some $3.5 million USD in fines. Once again The Pirate Bay (TPB) has risen from the ashes and remains one of the world's largest trackers.
Torrent Funk - This site has a crisp, clean interface and is currently free of advertisements. A growing torrent directory and search engine that uses an automated file verification method.
Torrent Pond - A meta-search engine that scours other sites and attempts to filter out bad and fake torrents.
TorrentReactor - Claims to be the oldest tracker site on the Web, site is newly redesigned.
Torrent Finder - Meta-search engine that checks over 160 torrent sites and trackers. Can be a little overwhelming because of the sheer number of results.
Music
Indie Torrents - Nothing but independent music here
JamToThis - Music related audio and video content
PianoSheets - Freely available sheet downloads
Punk Torrents - All punk, ska, and hardcore
RapHustle - rap music mixtapes and battles
Tapedown Mixtapes - Site for mixtapes provided by various record companies for promotional use
The Mixing Bowl - All dance, electronic you name it
Games
GameUpdates.org - Legally available game files including patches, demos, and mods.
My Gamebox - PC and console games
Ntorrents - All things Nintendo
The Poker Bay - Card playing related torrents
Underground Gamer - Retro gaming content
Software
Appz Universe - PC and Mac applications and software tutourials
LinuxTracker.org - All legally available software and virtual machines for linux platforms
SyncTheBits - Content for popular mobile platforms
Video
Animesuki - Strictly unlicensed English anime
Public Domain Torrents - A wide variety of movie torrents now in the public domain.
Mr Twig - Southpark
Son Of Shun - Political shows, documentaries, science
UK Nova - Programs from UK radio and TV
Adult
Empornium - Users are all about quality and won't tolerate crappy uploads or poor ratios
PornBay - Free leeching
Pure TnA - The name says it all lol
If you can't find it here there is a tracker mega list at TorrentKing. There are tons of sites listed there so you will have to filter through some trash but, I found some great ones too.