Introductions: Basic places to start on the .onion network.
 
ion's Hidden Wiki (Traditional wiki after Matt's went down) - The original Hidden Wiki is back up! It's a little outdated but it still contains all of it's misc. pages: http://kpvz7ki2v5agwt35.onion/wiki/index.php/Main_Page
Hidden Wiki Mirror - A direct mirror of ion's Hidden Wiki: http://ciz4t2plqme3e73a.onion/TheHiddenWiki/kpvz7ki2v5agwt35.onion/wiki/index.php/Main_Page.html
Censored Wiki - A censored Hidden Wiki mirror with better uptime. Hosted by TriPh0rce: http://3suaolltfj2xjksb.onion/hiddenwiki/
Hackbloc's Hidden Wiki Mirror - User edited mirror. Best alternative to the original Wiki as far as pages go: http://xqz3u5drneuzhaeo.onion/users/hackbloc/index.php/Mirror/kpvz7ki2v5agwt35.onion/Main_Page
Hidden Wiki Mirror - Heavily outdated. Use if you have to: http://7jguhsfwruviatqe.onion/index.php/Main_Page
OnionWiki - Share information about the technical side of Tor: http://ah5dm66duazqkz6h.onion/w/index.php/Main_Page
Core.onion - The long-standing introduction place for Tor: http://eqt5g4fuenphqinx.onion/
TORDIR - User-submitted links: http://dppmfxaacucguzpc.onion/
Sites Deep Web - Uncategorized list of links: http://ekwreugkil5ncyyh.onion/
Torlinks - Fast, moderated, and up-to-date without censorship. Essentially a mirror of THW but not in the Wiki format: http://torlinkbgs6aabns.onion/index.php
CircleServices - Domain hosted by mixie. Contains a lot of basic tools you'll find, like file hosting and a PM service: http://4eiruntyxxbgfv7o.onion/
Administrator's Index - Links some of his own services, like TSN, Hidden Image Site, OnionBookmark, etc: http://jm6miyk4tog63kqs.onion/
OnionBookmark - Keep track of your bookmarks on the Tor network. Choose whether to have your bookmarks public or private: http://x7yxqg5v4j6yzhti.onion/
 
 
Search engine: "Google" for Tor
 
TORCH - Supposedly indexes over 600,000 .onion sites: http://xmh57jrzrnw6insl.onion/
DuckDuckGo - Also an awesome clearnet search engine that respects your privacy. This doesn't actually search for Hidden Services, but it's similar to searching with a proxy: http://3g2upl4pq6kufc4m.onion/
DeepSearch - An alternate search engine that indexes Hidden Services: http://xycpusearchon2mc.onion/
The Abyss - Search engine run by Administrator, updated often. Now accepts user-submitted links: http://nstmo7lvh4l32epo.onion/
Torgle - The old search engine has been resurrected!: http://zw3crggtadila2sg.onion/torgle/
 
 
Bitcoin Laundry: Services for Bitcoin, a decentralized FIAT anonymous currency used in Tor. Obscure your Bitcoins' history.
 
Bitcoin Fog - I had a chance to test this out and it is legitimate. It's a great automated washing service: http://fogcore5n3ov3tui.onion/
(BitMix is a scam. At this time, Fog is the only reputable laundry service.)
 
 
Hosting file services: Hosts files.
 
SquareBoard - A public gallery of high-res images under 4MB: http://squareh565qgkioq.onion/
Onion Fileshare - 2GB upload file size limit!!!: http://f3ew3p7s6lbftqm5.onion/
qPasteBin - Hosts txt files, just like clearnet Pastebin: http://4eiruntyxxbgfv7o.onion/paste/
sTORage - Public file hosting. No CP. Anyone can delete files: http://utovvyhaflle76gh.onion/
ES Simple Uploader - Hosts images, docs, etc: http://i7hknwg4up2jhdkx.onion/
TOR Upload Service - A private place to hold files. Randomized URL and file name: http://ocrlwkklxt3ud64u.onion/
Tor Upload - Public file hosting: http://zmog4gnpn6wpooht.onion/index.php
Onion Image Uploader - Hosts image files: http://xfq5l5p4g3eyrct7.onion/
AnonyShares - Hosts rar/zip/etc archives: http://4eiruntyxxbgfv7o.onion/anonyshares.html
ImgZapr - Hosts image files: http://4eiruntyxxbgfv7o.onion/imgzapr/
 
 
Hosting websites: Information for .onion websites.
 
Freedom Hosting - Attacked by Anonymous, hosts a huge portion of .onion sites. Currently, invite only. Excellent uptime. GUI: http://xqz3u5drneuzhaeo.onion/
OnionHosting - Paid-for hosting by Administrator. Server-side: http://bj6sy3n7tbt3ot2f.onion/
SnapBBS - Hosts simplistic forums: http://4eiruntyxxbgfv7o.onion/snapbbs/
Tor WebDesign Guidelines - Doesn't host content, but has basic guidelines for making a site: http://wf4df37hrebhwzts.onion/
See the official Tor project site on information to host your own .onion site without a third party.
 
 
Chans/Imageboards - Kind of like 4chan and the likes. MAY CONTAIN QUESTIONABLE CONTENT. See the Chan page on the Cleaned Wiki.
 
Torchan - Birthday December 2011. Intelligent discussion, good admins, many boards. Reincarnation of the original Torchan. Moderated for child porn: http://zw3crggtadila2sg.onion/imageboard/
Anonchan - Birthday November 2011. Went viral after conception. Over 1000 posts in first month. Kind of cancerous now. Russians attacked the board, 404ing most threads. [s]Vulnerable to CP[/s] Moderated by me. /jb/ Jailbait, /b/ Random, /bm/ Black Market: http://od6j46sy5zg7aqze.onion/
Hidden Image Site - Moderated for CP. Mostly a dumping ground for spam: http://wyxwerboi3awzy23.onion/
TriChan - Good for bronies. Hosted by TriPh0rce. Non-CP: http://3suaolltfj2xjksb.onion/chan/
Thorlauta - Successor to Torlauta. Primarily Finnish, but has some nice added board features like a search bar. [s]Has an International (/ib/) board for English/other speakers[/s] Only Finnish at this time.: http://zqiirytam276uogb.onion/
Lukochan - A Russian/English discussion board in imageboard style. Extremely inactive but I noticed it has potential so I stuck it in here: http://562tqunvqdece76h.onion/Lukochan/
Deaths: RundaChan, Bobby's Board.
 
 
Boards: Mostly SnapBBS and phpBB. Normal forums.
 
ReddiTOR Reloaded - Reddit revived on Tor (2012/08/08): http://gmyzy5exjw4pimvf.onion/
Thieves Market - Cheap prices, nice goods: http://4eiruntyxxbgfv7o.onion/snapbbs/5595881d/
Onion Site Reviews - Review .onion sites in an organized way: http://4eiruntyxxbgfv7o.onion/snapbbs/5112d4d2/
Assassination Market - Famous SnapBBS board; mercenaries for hire: http://4eiruntyxxbgfv7o.onion/snapbbs/1acda566/
Underground Market Board - No escrow marketplace: http://4eiruntyxxbgfv7o.onion/snapbbs/1b82f13e/
Onionforum 2.0 - Forums for discussions. Meh discussion, Admins gone: http://65bgvta7yos3sce5.onion/
Onionforum 3.0 - Better than 2.0. Active Admin, and it's pretty great so far: http://wf74ekmmmgg2pe3v.onion/
RedditTor -  Reddit for Tor!: http://k6gsb4ibatcico35.onion/
Tor Help Forum - Basic convos and helpful for newbies: http://zntpwh6qmsbvek6p.onion/forum/index.php
Talk.masked - Very famous discussion board. Anon-posting: http://ci3hn2uzjw2wby3z.onion/
(Open to suggestions, e-mail me)
 
 
Networking: Social networking.
Torbook - Facebook for Tor. Has a public square for discussions: http://ay5kwknh6znfmcbb.onion/torbook/
Questions and Answers - A cool truth game: http://ajqaivfxtqy3fdlr.onion/qa/index.php
TorStatusNet - Similar to Twitter: http://lotjbov3gzzf23hc.onion/
Anonymoose Chat - Plain HTML chat: http://c2hluuzwi7tuceu6.onion/
multi.ver.se - Uncensored ocial network developed by the Chinese Pirate Party: http://ofrmtr2fphxkqgz3.onion/
 
 
Blogging/Revolutionary: Blogs on Tor. May contain some Revolutionary information. They pretty much go hand-in-hand in Onionland.
 
Wikileaks - If clearnet Wikileaks gets attacked, you know where to go to: http://isax7s5yooqgelbr.onion/
My Hidden Blog - Administrator's site. Frequently updated and has some interesting information. Also supports comments: http://utup22qsb6ebeejs.onion/
Tornado - User-supported blog. Polls, comments, and a forum: http://b6kpigzhrdhibmos.onion/d6/
Censor This! - A blog talking about censorship. It's not updated too often, but interesting nonetheless: http://cxoz72fgevhfgitm.onion/
ParaZite - Incredibly strange but well-made: http://kpynyvym6xqi7wz2.onion/
FREEFOR - A blog-ish site that contains a Wiki, forum, chat, and a couple more features: http://tns7i5gucaaussz4.onion/
Against Servants - A tl;dr about terrorism, foreign affairs, and fascist leaders: http://hlmrraadkb646464.onion/
Croat's Blog - Dead whistleblowing blog from Croatia. Shame: http://kv77v7n5kblz5tpw.onion/
Nekro's Onion Shanty - My blog! I use it as an update for Tor/General news, my list of Hidden Services, and I include some files you can download. LOST THE FREEDOM HOSTING PASSWORD. I'll have a new version of it up. Again...: http://guew63r73ur3iplh.onion/shanty/index.html
Area 51 Archives - A site that allegedly will be soon setting up a Wiki to mirror some of area51archives.com's content: http://u3dqz36dcvhwd7kv.onion/
 
 
Email/Messaging: Communication.
 
TorPM - Tor private messaging: http://4eiruntyxxbgfv7o.onion/pm/
Tor Mail - Email services. *@tormail.org: http://jhiwjjlqpyawmpjx.onion/
PrivacyBox - The Tor version of PrivacyBox.de. Seems like a great e-mail service: http://c4wcxidkfhvmzhw6.onion/index.en.html
 
 
Hax: Hacking, cracking, phreaking, doxing, security, etc.
 
HackBB - Forums for hacking, hosts some content. Great community: http://clsvtzwzdgzkjda7.onion/
Hashparty - Cracking site: http://3terbsb5mmmdyhse.onion/
Weird and Wonderful Old Stuff - Collection of old DOS and Windoze software: http://xqz3u5drneuzhaeo.onion/users/dosbox2/
Doxbin - A large index of personal identifying information. User-submitted. Similar to /i/ or personal army or the trends you see on Pastebin: https://doxbinumfxfyytnh.onion/
Requiem - Remove Apple's DRM security. Confirmed by many users as legitimate: http://tag3ulp55xczs3pn.onion/cgi-bin/ssi/index.shtml
 
 
Media: Hosts media content. May want to see "Hosting file services" for misc.-related content.
 
Newzbin - Warez site: http://sc3njt2i2j4fvqa3.onion/
LiberaTor - Military, anarchy, weapons, etc stuff: http://p2uekn2yfvlvpzbu.onion/
Tard's Library - User-run ebook site. Lots of content: http://xsin4xbme24aatvk.onion/
The Tor Library - Over 48GB of books on all kinds of subjects: http://am4wuhz3zifexz5u.onion/
NoReason's Site - Has loads of info and pdf files on different subjects. High down-time, but it occasionally goes up. It's an amazing site: http://fkyvwpu7ccsorke2.onion/
Lossless Audio Files - Music; great sound quality: http://wuvdsbmbwyjzsgei.onion/
Fenergy - Has some ebooks and links on energy resources: http://jpmgvki37zcy7o35.onion/fenergy/
The Pirate Bay - The .onion mirror of The Pirate Bay. If TPB is censored in your country, use this!: http://jntlesnev5o7zysa.onion/
 
 
Marketplaces: Places where you can buy stuff! Or research a particular illegal subject (ahem, drugs).
 
Silk Road - Infamous on the news. Excellent products and (mostly) reliable sellers. This is the REAL AND ONLY LINK!!!: http://silkroadvb5piz3r.onion/index.php/silkroad/home
Black Market Reloaded - Excellent products, smaller than Silk Road. Doesn't require a fee to be a seller: http://5onwnspjvuk7cwvk.onion/
BMR Forums -  Discussions: http://fec33nz6mhzd54zj.onion/
Silk Road Forums - Discussions: http://dkn255hz262ypmii.onion/index.php
TorDrugResource - Chemistry, pharmacology, cultivation, and lots of other information on different types of illicit substances. Mostly PDFs: http://y47ylcppnh3afqk4.onion/
The Armory - Silk Road's new market for guns and ammunition. Buy Sasha (TF2 reference): http://ayjkg6ombrsahbx2.onion/silkroad/home
 
Pornography: Normal adult sites on Tor.
 
Starfuckers, Inc. - Celebrity nudes: http://mvdezygqixx3ucpl.onion/
Adult Pictures - A large album of various porn pictures: http://54dgeda4ik6iypui.onion/
bitpron - Buy porn with Bitcoins. Cheap prices. Unconfirmed: http://eryedcdjhwufuelr.onion/
 
 
Misc: Cool websites that don't fit any of the above.
 
Long Live the enV2 - A beautifully weird site about the LG enV2. I've got no idea why this was created in the first place, but...: http://iwdmsbpxclyjhi4e.onion/index.html
Carson - It's a poem. But a good poem. Yep: http://carson27rcopqmms.onion/
C'Thulhu - Infamous assassin group on Tor. *Highly* doubt it's legitimate, but interesting nonetheless: http://iacgq6y2j2nfudy7.onion/
Beneath VT - Information on the tunnels under Virginia Tech: http://74ypjqjwf6oejmax.onion/
Indymedia Keyserver - A place to distribute your PGP public key: http://qtt2yl5jocgrk7nu.onion/
Therapy - Talk about your problems with this cleverbot-esque robot. It used to be named "Eliza", but now the "primary therapist" is a Dr. Robert: http://nel2xugswcy7qv7r.onion/
Human Experiments - "We go, where few dare". Supposedly collects data from torture sessions. Obviously fake, but still a famous landmark: http://xqz3u5drneuzhaeo.onion/users/experiments/
Exit The Matrix - Currently the only browser game on Tor! Take the red or blue pill. Unfortunately, we still need to find a home for it, so for now, it will be hosted on sTORage: http://utovvyhaflle76gh.onion/sTORage/exit_the_matrix/index.html
Mariana's Web - Experience the forbidden: http://dx37guvtyy7wil3n.onion/index.html
Gateway - An i2p proxy! It routes you through the i2p network and allows you to visit eepsites. Read more about i2p @ http://www.i2p2.de/. For a large list of i2p sites, visit the eepsite http://identiguy.i2p: http://6dyi4t72u7y6g763.onion/