The first one which many people who play pokemon may not about is a character called "Looker" This one is probably the most likely to be a reference of the three as there are numerous little parallels to The Tenth Doctor.
As you can see right off the bat from the link, he looks a lot like the Tenth Doctor, but that alone would not count for much. There are a number of other things to support this theory.
-When the character known as "Looker" introduces himself he talks in an odd manner and says he goes by that code name. At no point is an actual name given, much like The Doctor.
-Looker is introduced in a pokemon game in which the 3 pokemon the story revolves around have the power to influence time, space, and dimensions. His goal, along with the player, is to stop a group of bad guys from gaining control of them. Something the Doctor does regularly.
-The only pokemon Looker is known to own is called Croagunk. If you look at it, all its colors are similar to that of the TARDIS. Mostly blue, matches the TARDIS exterior, black and white matching places with text, orange and yellow matching the interior on the exterior. While the pokemon itself has no relation beyond that and is in no way based off the TARDIS, it is still a bit odd that they gave him the pokemon that coincidentally matches the iconic time machine. It should also be noted that Looker doesn't use it to battle at all, which may be parallel to The Doctor not liking fighting.
The next possible reference is a pony in the newest version of the My Little Pony franchise called "My Little Pony: Friendship is Magic". Now this, is actually a pretty great cartoon... probably not so much the older ones. Its got quite a following, a LOT of GUYS and girls outside of the original target demographic due to its good writing and characters, and also being by the creator of the Powerpuff Girls. As such one of the backgroud characters with no real official name has been given the fan-name "Doctor Whoof". He has been speculated to be based on The Tenth Doctor because of his spike mane being dark brown and his coat being brown along with a Hour-Glass symbol on his flank. (all ponies gain a symbol which defines them to some extent).
Here are two videos of him:
(some fan made intro spoof, he appears at 0:28, no British accent unfortunately)
(warning, I take no responsibility if this song get stuck in your head. He makes quite a few appearances starting at 0:40 along with the fan named pony "Romana" who is blue with a Hour-glass mark and appears starting at 1:19)
And a link on the MLP:FiM wikia with a bit of info on him (need to scroll down some) http://mlp.wikia.com/wiki/Background_pon
Hes probably the second or third most popular background character in the show. With a number of good fanart, fanfiction, and marcos.
The last reference is in another DS game, Dragon Quest IX. This reference is likely only in the English version as the translators or localization team for the series recently have a hard on for making everything puns or references, which is actually quite annoying. However one good thing to come out of it is a Dalek reference.
One of the "Boss monsters" in the optional post-game dungeons is a giant one eyed robot. The design of the robot itself, called The Trauminator (a Terminator reference), has nothing to do with a Dalek, but rather the dialogue that its given.
""Bzzzt... Dzzz... Must-trauminate...
In this game you also gain titles for your character after completing certain tasks or challenges. The character that awards you said titles usually his a bit of dialogue on the subject of the title. The title relating to defeating this monster robot has the character awarding you the title say "Exterminate! Exterminate!"
Well, hope you all thought these were as cool as I thought they were! And I hope I explained the references well enough to people who aren't fans of said franchises.
Any references you all know of that aren't as well known or obvious as something like Four in Family Guy's Blue Harvest?