Donna Noble

Soulbond (You may pair this creature with another unpaired creature when either enters the battlefield. They remain paired for as long as you control both of them.)
Whenever Donna or a creature it's paired with is dealt damage, Donna deals that much damage to target opponent.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Graham O'Brien

Paradox — Whenever you cast a spell from anywhere other than your hand, create a Food token. (It's an artifact with "{2}, {T}, Sacrifice this artifact: You gain 3 life.")
Doctor's companion (You can have two commanders if the other is the Doctor.)

Jhoira's Timebug

{T}: Choose target permanent you control or suspended card you own. If that permanent or card has a time counter on it, you may remove a time counter from it or put another time counter on it.

Amy Pond

Partner with Rory Williams (When this creature enters the battlefield, target player may put Rory into their hand from their library, then shuffle.)
Whenever Amy Pond deals combat damage to a player, choose a suspended card you own and remove that many time counters from it.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Jhoira of the Ghitu

{2}, Exile a nonland card from your hand: Put four time counters on the exiled card. If it doesn't have suspend, it gains suspend. (At the beginning of your upkeep, remove a time counter from that card. When the last is removed, you may cast it without paying its mana cost. If it's a creature, it has haste.)

The Tenth Doctor

Allons-y! — Whenever you attack, exile cards from the top of your library until you exile a nonland card. Put three time counters on it. If it doesn't have suspend, it gains suspend.
Timey-Wimey — {7}: Time travel three times. Activate only as a sorcery. (For each suspended card you own and each permanent you control with a time counter on it, you may add or remove a time counter. Then do it two more times.)

K-9, Mark I

Negative — As long as K-9, Mark I is untapped, other legendary creatures you control have ward {1}.
Affirmative — {1}{U}, {T}: Target legendary creature can't be blocked this turn.
Doctor's companion (You can have two commanders if the other is the Doctor.)

Clara Oswald

Impossible Girl — If Clara Oswald is your commander, choose a color before the game begins. Clara Oswald is the chosen color.
If a triggered ability of a Doctor you control triggers, that ability triggers an additional time.
Doctor's companion (You can have two commanders if the other is the Doctor.)