This list is by no means complete, some of the sites go up and down every day as well.
General info:
*Hidden Wiki (down at the moment):
http://kpvz7ki2v5agwt35.onion/wiki/index.php/Main_Page
Site directory:
*TorDIR:
http://dppmfxaacucguzpc.onion/ <-- if you want to get a feel for sites on Tor, START HERE
*Circle:
http://4eiruntyxxbgfv7o.onion/
*Torch (a search engine):
http://xmh57jrzrnw6insl.onion/
Drug-related and general paraphernalia sales:
*Silk Road:
http://silkroadvb5piz3r.onion/silkroad/home
Message boards (like 4chan):
*Torchan:
http://zw3crggtadila2sg.onion/imageboard/
*Anonchan:
http://od6j46sy5zg7aqze.onion/
Some kind of message board/social network hybrid:
*Torbook:
http://ajqaivfxtqy3fdlr.onion/torbook/
*Torsquare:
http://ajqaivfxtqy3fdlr.onion/torsquare/
Hacking, carding forum:
*HackBB:
http://clsvtzwzdgzkjda7.onion/
"Libraries":
*Tor Library:
http://am4wuhz3zifexz5u.onion/
*LiberaTor (contains a bunch of random military-related links):
http://p2uekn2yfvlvpzbu.onion/
Tor mail service:
*Tor Mail:
http://jhiwjjlqpyawmpjx.onion/
*TorPM:
lol forgot the link