Twilight's family tree by TobyandMavisforever on DeviantArt (original) (raw)
Twilight's one was much more simple than Fluttershy's or Applejack's...
Twilight Velvet and Night Light - No one would have ever dreamed Twilight Velvet and Night Light would have ended up together. Miss Velvet loved high rising adventure while Night Light was more a professional stallion. But, something clicked between them, and they had two of the most accomplished ponies they could have ever dreamed of: The Princess of Friendship, Twilight Sparkle, and Captain of the Royal Guard and Prince of the Crystal Empire, Shining Armor.
Carrot Cake and Cupcake - I've yet to figure out something for these guys, but I think their relationship is an adorable one.
Twilight Sparkle and Flash Sentry - Twilight wasn't exactly looking for a romance, but luck would have it that she ran into a cute guy in the mirror world called Flash Sentry. When she came back, she saw the pony version of him. At first, she tried to brush it off like it was nothing, but on one particular day she, Spike and the girls were helping Vincent and Fictionary connect the dots about their family history. Their trip took them to the Crystal Empire where they found out that Flash and Vincent had the same parents, Fictionary was actually their half-sister as were twins First Base and Tender Taps! Long story short, this pulled a massive strain on the family (I'll get into depth with this with Flash's side of things), Twilight started to console Flash during this time and really got to know him as a pony. They did various things together like watching the stars, going for short distance flying, reading books and even having lunch together sometimes. The two of them started to form a friendship during this trialling time, and eventually Twilight, Sunset, Butterscotch, Apple Bloom and Sunny Daze were able to bring all the siblings back together. After all was said and done, Twilight and Flash really started to grow affection for one another, and it was much deeper than Twilight's crush she had on the mirror Flash. They happily married and Flash became the co-ruler of Equestria alongside Twilight.
Shining Armor and Cadence - Read the comic Neigh Anything and watch A Canterlot Wedding, The One Where Pinkie Pie Knows and The Crystalling as to how Cadence and Shining's love story came to be.
Flurry Heart and Pound Cake - It started off as a simple friendship, with Flurry Heart being on playdates with Pound and Pumpkin every once in a while when they were babies. Then, when they were school aged foals, Pound Cake and Pumpkin Cake often asked Flurry to come to Ponyville and they would go to the Crystal Empire for a visit. Pound, Pumpkin and Flurry became very close with each other, and even became the next generation CMC alongside Coral Currents (Sandbar's little sister), except with an alicorn instead of two earth ponies. At first, everypony made a huge deal about Flurry visiting Ponyville all the time, the Crystal Princess' daughter who just happened to be born an alicorn? Poor Flurry was overwhelmed with attention and praise, but thankfully Pound, Pumpkin and Coral Currents kept them at bay. As time went by, Flurry and Pound started gaining crushes on each other, much to Pumpkin and Coral Currents' amusement. This turned out to be a real love story, as Flurry and Pound got married as adults and Pound moved to the Crystal Empire, leaving Pumpkin to run the bakery with her wife Coral Currents, which is an ironic twist in of itself.
Update: Twilight's family is now related to Lilymoon's family.