There has been much speculation on whom, where and why the Parents of the mane six characters are not seen more often. I think that while the personalities of these ponies can only be guessed at, their location and reasons for their absence can be more readily assumed.
Twilight Sparkle's parents presumably live in Canterlot, since Twilight herself was born and raised there up until the beginning of the series, where she permanently moved to Ponyville. Similarly, Rainbow Dash and Fluttershy's parents probably live in Cloudsdale.
Pinkie Pie's parents would likely still be living on their Rock Farm. However the nature of their one appearance in the show (One of Pinkie Pie's stories, that ended with 'And that's how Equestria was made' no less) leaves the viewer wondering just how much of Pinkie's story is actually true and whether there even is a rock farm. If there is, that's where Pinkie's parents live, if not, then I can't say for sure but they probably live a small town similar