The character shown is another background character that has taken on a life of its own, not unlike my precious Derpy. This was just another cloned pony with a random cutie mark, in this case, an hourglass (if you look close, you can see him in the background of the party scene in the first episode). Nothing to it.
It was about the time the episode "Winter Wrap-Up" ran that things took off. He was featured prominently and everyone got a good look at him. A poster on one of the chans cracked the "My Little Time Lord" joke, resulting in the Motivational Poster that led off my post. Then, someone came up with the name "Doctor Whooves". There's a key difference between Doctor Whooves and Derpy, though -- Derpy has not only become canon, but she fits in the series' overall structure. A Time Lord shaped like a pony? That's tougher to incorporate.
And so, Doctor Whooves is the second biggest running gag in the fandom. He is primarily associated with Matt Smith because of his hair, and fanfics with the character frequently have him say, "I'm a pony now. Ponies are cool." Because the episode was still being done before everyone started noticing the Doctor, a subsequent episode featured a clone with Pegasus wings (it's during the flying competition), prompting one poster to joke, "Well, some regenerations are better than others." Another pony that appears later on that some fans speculate is another regeneration of the Doctor. This is a blue pony with a bow tie (but still an hourglass on his flank) that they say resembles the fifth Doctor, Peter Davidson.
Hasbro, I have to say, is really sporting about all this. During the San Diego Comic Con, there was a Friendship Is Magic giveaway poster, and Doctor Whooves was featured quite prominently on it. Although I'll be far more impressed they make a Derpy doll in time for Christmas.
Now, we get to the general notice. How many of you are familiar with the term "fanime"? It's fan-made anime, sort of like the proper definition of doujinshi (the word means "fan art" and covers any sort of fanfic, not just hentai. In Japan, doujinshi is about 50% stuff that is fanfic and 50% porn. With American audiences, those numbers skew to more like 10% fanfic and 90% porn. Just making sure no one thinks I'm equating what I'm going to write about with hentai). With the advent of digital editing on the cheap, cheap animation tools, or even just using game engines (machinema, such as Red Vs. Blue and several fan made Sam And Max shorts), several fanime have been made, such as the lousy Care Bear Stars, a mash up of Care Bears and Sailor Moon (the art is pixelated and clearly done with MSPaint).
Well, I recently became aware of a group calling itself Bronytoons that is looking to make a Doctor Whooves fanime. Check this out...
Bronytoons says that they are looking for someone to do the voice of Twilight Sparkle for their Doctor Whooves. They are also looking for additional voice actors, artists, animators, writers, etc. If you want to get in touch with them, the email address is Bronytoons@gmail.com
Let me know what shakes out. Hell, I'm half tempted to try and pitch in as well.