The Uncle/Niece thing is purely from Young Justice, which had a slightly different version of Miss Martian. She's always been a White Martian in the comics, sent to Earth by her parents to escape the Martian Civil War, and initially pretended to be a Green Martian as part of the Teen Titans. One of her main storylines involved her encountering and defeating an evil future version of herself that gone full White Martian, only to have elements of her evil version merge with herself which she has to overcome.
Miss Martian is a fairly recent character to the comics, only coming in shortly after the Infinite Crisis storyline (mid-2006), and I can't seem to think of her doing too much outside of the Teen Titans books. A couple of cameos here and there in Supergirl and Batgirl books, but not much else. I'm not even sure if she's been introduced yet in the New52 continuity yet. The main thing I remember about her is that she lived in Australia for a while, because the Australian Outback reminded her of Mars. I always that was pretty cool, because we don't get too many super-heroes down here. We're claiming her as an Aussie!