Knights of Time and Space will be used in an upcoming episode.Because it's to Epic-Awesome for those two to not use. Listen! Episode Six is supposed to deal with Derpy and the Doctor argueing and their friendship being strained to the breaking point. Having this song at the very end would be the perfect way to end the episode and show their restored and stronger than ever friendship at the same time in an And the Adventure Continues sort of way.
Ditzy's selective immunity to the Psychic Paper will become a plot point.Episode 5 revealed that the Psychic paper only works on one eye at a time. It would be perfectly befitting both source materials by setting up a future plot point as a seemingly one-off gag. Clearly The Master will show up with the same item and the only pony who either believes The Doctor or sees through the ruse will be Ditzy, because she's partially immune to it.
Ditzy's voice will change at some point.It's got to, what with The Last Roundup and all.
The Blue Unicorn that the Dr. talked to is his future incarnationHe knows quite a lot about electrical surges…especially since they don't exist in Equestria.
Derpy has romantic feelings for the DoctorConsidering the fact Bald Dumbo Rat (Voice of Derpy)runs a tumblr ask-blog called "Doctor Obsessed Derpy" (lovestruck-derpy.tumblr.com) and whenever she dubs it, she acquires the help of Keikoandgilly (The Doctor), the things in the blog should become relevant sometime in the series. Some may even doing an adventure on Hearts and Hooves Day considering they were seen together then.
Doctor Whooves and Assistant reads this page
Possible 2nd companion in futureOn the Whoovesnassistant tumblr, the Doctor mentioned a character named "Cuckoo Clock" stating that he'd never forget the name, possibly referring to a future important pony/companion (Possibly blue unicorn?)
The Pegasus Doctor from "Sonic Rainboom" will be explained in a later video.
Time Turner will be a Line-of-Sight Name, just like John Smith was.Ditzy will be improvising just like Jamie was in The Wheel in Space.
The Doctor is the reason Derpy hasn't been in any season 3 episodes so far.
Ditzy is one of Clara's incarnations.
One of Pinkie Pie's ancestors invented the can openerWho else could create a useful device that could open something that hasn't been invented yet?