The doctor is The Doctor.Let's see here... Eccentric personality? Check. Pacifistic personality despite action-type lifestyle? Check. Knows major historical figures? Ben Franklin and Dracula, so check. Has sidekicks? Judy and Gordito, another check. Expert in things that fall outside normal human experience? Check. Being riddled with bullets may well have cost him a regeneration rather than just being something he survived though sheer force of will, but we can't tell if his face looks different because he's wearing a mask.
Webcomic/UnsoundedMurkoph is an insane Time-Lord. He's disturbingly knowledgeable, seems to know the inner-workings of the reality of Unsounded, and could have been trapped in the Khert when he was fleeing from the Time-War.
Kin is a Time Lord.
Riku is a Time Lord.Namine just said she thought Riku was dead, and Riku said he was, and he would explain later. Clearly, he just regenerated.
Xemnas is a Time Lord.His wacky coat is his TARDIS. And a central part of his plan is to take Sora back in time. Red XIII is his current companion, Larxene was once but she was convinced into staying with the main cast.
Susan is a Time Lord.Diane is one of her regenerations, naturally.
Otto Wisebottom is a Time Lord.After all, he's invented a time machine!
Lucrezia is a Time Lord.The Master, actually, being evil and all. She has a time machine!
Agatha and/or Gil are Time LordsTrope Law Fourteen demands it!
Dr. Disaster is a Time Lord.Annie describes him as "the saviour of the universe, apparently" on the old version of the Cast Page. His simulations are combat training for an inevitable alien invasion. The students' strange accommodations were his idea — protection from aliens that can't scale heights.
Starface is a Time LadyDon't know what her TARDIS is, but come on. How else does she keep appearing at the final battle of every Mother game to see that the main character performs his heroic deed?
Cale is a time lordRichard is his tardis
Comments on a Postcard was/is created by a Time Lord.The details given about the artist's personal life are unbelievably inconsistent, especially with regards to when the comic was created. All of the origin stories are true —- the Time Lord in question has been all the people mentioned in them, and the forum user who suggested it is just the current incarnation.
The entire storyline of Misfile is a prequel/origin story for Doctor WhoRumisiel is obviously a pre-William Hartnell version of the Doctor before he got all clever and the Tardis. Cassiel and Vashiel are early versions of The Rani and The Master explaining their Ripple-Effect-Proof Memory. "Heaven" is Gallifrey and the Celestial Depository with it's reality altering, omniscient and omnipotent files is its central computer. Even the absent God story corresponds to the absence of Rassilon and the whole Satan's takeover thing was the first Time War. Ash and Emily are obviously prototype companions.
Jade (gardenGnostic) in Homestuck is a Time Lord.It would explain how she somehow has knowledge of future events in the storyline.
Pickle Inspector is every Time Lord.By default, since all matter in the universe is made up of subatomic-sized time-displaced reincarnation of PI.
Spades Slick is a Time Lord.Because he's everyone.
Lord English is The Doctor himself.It has already been speculated once, but we got a clearer picture now.
Dave and Aradia are Time Lords.OH WAIT.
uu is a Lord of Time, and whatever chat program he uses to jeer at people is his TARDIS.
The MitD is Half-Tarrasque, Half-Time LordThe pink umbrella is his TARDIS, which explains how a Tarrasque fits under it.
Oasis is a pyrokinetic Time Lord.With exceptional control over the physical aspects of her regeneration, but very little mental stability.
Riff is a Time Lord.Think about it. The DFA is probably his TARDIS.
Bun-Bun is a Time LordThe Master, or one of a similar alignment. He's nearly unkillable, he has regenerated from near-death several times, and the switchblade is his TARDIS. Oh, and there were those (two) times that he was thrown out of the space-time continuum. Only a Time Lord could survive that.
All the various Deaths are dead Time Lords.They are able to travel through time at will, and are used to experiencing events in a non-chronological sequence as a result. Also, the Head Death knows about time paradoxes and how they can lead to the destruction of the universe. Multiple paradoxes happening simultaniously in a number of different times fits with the Whoniverse's timey-wimey ball, and implys that only one, or just a couple of paradoxes would not be a problem.
The Beret Existentialist is a Time Lord.Like most xkcd characters, he has no name, but displays many personality traits similar to The Doctor such as moments of Cloud Cuckoo Lander -ness, and very philosophic tendencies. Also, recently, the ability to grow infinite wings. Given the style of his Nice Hat, possibly a reincarnation of Jamie from MythBusters.
Jack Fortinbras is a Time Lord.His character page suggests that he might be one. How else does he have time to get straight As in Physics and captain the Varsity Rugby team?