We've gotten to the end of Season 2 of Louie on Netflix, and unfortunately Season 3 is still Missing in Action on the service. Season 2 ran from June to September 2011 and was posted to Netflix in June 2012. Season 3 ran June to September 2012, so it stands to reason that it might be June 2013 when Season 3 comes to Netflix.
In the meantime we're ordering Season 3 on Amazon Instant for 20 bucks instead of waiting: Louie Season 3 on Amazon Instant (This link includes a code to tell them we sent you and helps us keep the site running). HD is also available, but they aren't free with Prime. We'll post an update as soon as any new info gets posted. We don't recommend clicking any links from a search for "Louie Season 3" as most are scam sites supposedly selling the episodes, viruses claiming to be a download link, or spoilers about the season finale.
Fortunately Seasons 1 and 2 were In Order.