Ascended Fanon: A few examples arose even before the game hit alpha. The developers have a good relationship with the game's early/crowdfunding community, and early community in-jokes have already begun to make their way into the actual development process.
Space Lube: The Geddon System, concept introduced during the crowdfunding campaign, introduces a commercial trade good - a high-quality space engine lubricant called "Planetsblood", produced and refined from one of the planets' active underground volcanoes. A possible tribute to the site's chat room regulars and the then-frequent devolution of live chat content to jokes, references, and innuendo about space lube and everything you'd want or need it for on a long spaceflight.
"Space Whale", an asteroid shaped like a whale from Earth. A huge attraction and tourist trap in the Nemo system. Obviously inspired by the chat meme of Space Whales.
"Lore Builder" is the invocation of this trope, with the developers selecting segments of the universe that haven't been fleshed out and choosing the best submissions.
The ship captain from the MISC Freelancer commercial has been named "Bob McCutcheon, Totally Legitimate Freighter Captain" by forum-goers.
Dueling Games: With Elite: Dangerous, the latest entry in the Elite series, though Chris Roberts personally backed Elite: Dangerous's Kickstarter and encouraged his own backers to do the same, and David Braben of Elite is an alpha backer of Star Citizen.
Schedule Slip: The initial intended release date was November 2014, but that has since been pushed back to early 2015.