The largest independent content sites
Quantcast makes it easy to see the largest one million sites in the US (by traffic). There's a signficant consolidation going on, with the vast majority of popular sites being owned and controlled by larger, public companies.
Because online traffic follows, as most things do, a power law curve, the top 100 sites account for a huge amount of overall web traffic–probably more than the next 900 sites combined.
After removing public companies and those that only do commerce, here are the [fewer than] thirty independent companies on the top 100:
facebook.com
twitter.com
wikipedia.org
answers.com
wordpress.com
craigslist.org
tumblr.com
whitepages.com
manta.com
photobucket.com
yelp.com
wikia.com
hubpages.com
inbox.com
squidoo.com
drudgereport.com
coolmath-games.com
city-data.com
urbandictionary.com
wunderground.com
chacha.com
bleacherreport.com
twitpic.com
deviantart.com
cafemom.com
zimbio.com
typepad.com