* Rainbow Dad and Night Light (Rainbow Dash and Twilight's fathers) are both bisexual and used to be in a relationship back in college. They broke up at some point, and later in their lives met their respective wives and had their much more famous children. They know their daughters are friends with the other one's daughter, but Twilight and Rainbow Dash don't know about their father's history.
*The bat ponies (the bat-winged royal guards from the beginning of Luna Eclipsed) are another race of pony. They are fully nocturnal, have excellent night vision (thanks to their cat-like eyes), and they come from a gothic Transylvanian-esque culture. But other than that, they are pretty much pegasai with differently-structured wings.
*Caramel (famous for being shipped with Big Macintosh) is one of quadruplets. He has an identical twin brother (who lives in Appleloosa and later moved to Canterlot, as seen in Over a Barrel and A Canterlot Wedding), a fraternal twin brother (who looks like Big Macintosh, as seen in the Season 1 opening), and a fraternal twin sister (who lives in Appleloosa, as seen in Over a Barrel). Their father is Doctor Stable (the unicorn doctor from Read It and Weep).
I have more, but those are the first three that come to mind.