Seems more common since 2005.

Eleven info dumping Craig. Eleven making people call asleep. Twelve doing likewise. Ten memory-wiping Donna. Ten basically flying in tEoT.

Terror of the Zygons. The Doctor manages to hold his breath for several minutes in a vacuum chamber.

Four To Doomsday. The Doctor manages to spacewalk from a freighter airlock to the TARDIS wearing only a space helmet and no spacesuit.

Survival. The Doctor subdues an ex-army gym instructor with a single finger to the forehead.

Wow. Three great classic examples!

10th Doctor surviving that fall in TEOT - I see that was mentioned.

Erm...3rd Doctor shutting his body down in...was it Planet of the Spiders? Or was he just meditating to shrink his body or something? To escape from his spider web sleeping bag? can't remember now, probably getting it all muddled.

Lots of telepathy based stuff in the new series, but it was there in classic too. Susan was the first gallifreyan we saw as telepathic so I suppose that's been a thing from the beginning.

Surviving fatal injury by regenerating his entire body - that's happened a few times now I think.

Can't think of too much else superhuman in the new series. And maybe the tenth Doctor had tiny airbags built into his suit?

The First Doctor's regenerating trousers?

Not my favourite moments tbh. They don't make sense. As in, rather like time travel itself, why doesn't he use such special abilities all the time? For example, If he's able to survive falling great distances, why was 7 so perturbed when he was hanging by his umbrella?

You would survive a shin kicking contest, but your post match broken legs wouldn't perturb you?

I've not read the other posts yet because i wanted to see what I could think of on my own...

I'm unable to recall actual episodes I'm afraid but the list would be:

Psychic powers, mainly telepathy.

Inhuman Endurance, including an ability to survive extreme falls (strangely the 4th Doctor lost this ability, although he did share Victorian Clara's uncanny attribute of not bleeding at all when dying from a great fall).

Extremely slow aging process.

Incredible co-ordination (when playing sport for example)

Superhuman breath-holding.

The ability to recover physically from trauma by going into a coma-like state.

Regeneration (obviously), including, latterly, partial regeneration (growing back limbs etc). He can also use this ability to heal others.

Superhuman luck (exhibited in every episode of Doctor Who ever).

Thanks Tom! I suspect Clara's lack of blood may partly be down to it was a Christmas special watched by many children.

Of course. My tone was very tongue in cheek of course

I just remembered another: an inhuman tolerance for radiation... sometimes.

Also: psychic 'jolts' that can render a man unconscious.

Instant hypnosis: "Talons of Weng Chiang".
More extended air deprivation: "Ark in Space", "Two Doctors"

Four's very handy respiratory bypass system - very useful in a tight squeeze when throttled by robot Mummies.

Three and Four also managed to put themselves into self-induced comas on a number of occasions.
The Monster Of Peladon, after being assaulted by the Security Disco Lights, has one such instance (though maybe the Doctor had just seen the scripts for the rest of that story and simply shut himself down to spare himself from further agony....). Another was when the virus was attempting to take him over in the Invisible Enemy.

Incidentally, the clear way of reviving a comatose Time Lord is to lay your head on their chest and sob. Your tears soaking said Time Lord's shirt will somehow have magical healing properties and will undoubtedly cause you say "Oh Doctor, I thought you were dead".

Ambassadors of Death: "transmigration of object"

The Seventh Doctor hypnotises a soldier by pressing a finger to the man's forehead (Curse of Fenric) and fixes Ace's twisted ankle by twitching her ear (Remembrance of the Daleks). Do these count?

10th Doctor ridding his body of radiation via his foot.

Well, 10 fell out of that spaceship, through a domed glass roof without any apparent injury, so why would 7 worry about a different fall from a great height. That's my point.

I'm sure it's not the strongest example of inconsistency, but it's the best I could come up with at short notice. There must be plenty of "He could do that then, so why didn't he do that here?" moments.

These special abilities come and go at the whim of the writers, just like fixed points, changeability of history or non-changeability of history. There's no internal logic or consistency, which, I admit, is problem for DW in many other areas too.

Why did the sixth Doctor regenerate after falling off his exercise bike ?

The 9th Doctor walking through the fan in The End of the World?

Indeed. Or when 4 fell off Jodrell Bank Radio Telescope.

Sexual exhaustion.

Dear God, No!!
Mel was his companion at that point. Mel! What on earth are you suggesting?
It's too horrible to contemplate...

a.k.a Showing off.

He was too heavy for it?

Think about it - why else would we not see what really triggered the regeneration? The subtext had to be that it was to disturbing for us to know...