Wibbly-wobbly, Timey-wimey

Time travel. (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.)
Draw a card.

Unlikely Meeting

Search your library for a Doctor card, reveal it, put it into your hand, then shuffle.

Twice Upon a Time

Cast this spell only if you control two or more Doctors.
Take an extra turn after this one. Exile Twice Upon a Time.

Twice Upon a Time // Unlikely Meeting

Aminatou's Augury

Exile the top eight cards of your library. You may put a land card from among them onto the battlefield. Until end of turn, for each nonland card type, you may cast a spell of that type from among the exiled cards without paying its mana cost.

Scroll Rack

{1}, {T}: Exile any number of cards from your hand face down. Put that many cards from the top of your library into your hand. Then look at the exiled cards and put them on top of your library in any order.

Inspiring Refrain

Draw two cards. Exile Inspiring Refrain with three time counters on it.
Suspend 3—{2}{U} (Rather than cast this card from your hand, you may pay {2}{U} and exile it with three time counters on it. At the beginning of your upkeep, remove a time counter. When the last is removed, you may cast it without paying its mana cost.)

Inevitable Betrayal

Suspend 3—{1}{U}{U} (Rather than cast this card from your hand, pay {1}{U}{U} and exile it with three time counters on it. At the beginning of your upkeep, remove a time counter. When the last is removed, you may cast it without paying its mana cost.)
Search target opponent's library for a creature card and put that card onto the battlefield under your control. Then that player shuffles.

Arcane Signet

{T}: Add one mana of any color in your commander's color identity.

Chaos Warp

The owner of target permanent shuffles it into their library, then reveals the top card of their library. If it's a permanent card, they put it onto the battlefield.

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.

Archon of Cruelty

Flying
Whenever Archon of Cruelty enters or attacks, target opponent sacrifices a creature or planeswalker of their choice, discards a card, and loses 3 life. You draw a card and gain 3 life.

Temporal Trespass

Delve (Each card you exile from your graveyard while casting this spell pays for {1}.)
Take an extra turn after this one. Exile Temporal Trespass.

Rotating Fireplace

Rotating Fireplace enters tapped with a time counter on it.
{T}: Add an amount of {C} equal to the number of time counters on Rotating Fireplace.
{4}, {T}: Time travel. 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.)

Sakashima the Impostor

You may have Sakashima the Impostor enter as a copy of any creature on the battlefield, except its name is Sakashima the Impostor, it's legendary in addition to its other types, and it has "{2}{U}{U}: Return this creature to its owner's hand at the beginning of the next end step."

Talisman of Dominance

{T}: Add {C}.
{T}: Add {U} or {B}. Talisman of Dominance deals 1 damage to you.

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.)

Talisman of Indulgence

{T}: Add {C}.
{T}: Add {B} or {R}. Talisman of Indulgence deals 1 damage to you.

Auton Soldier

You may have Auton Soldier enter as a copy of any creature on the battlefield, except it isn't legendary, is an artifact in addition to its other types, and has myriad. (Whenever it attacks, for each opponent other than defending player, you may create a token copy that's tapped and attacking that player or a planeswalker they control. Exile the tokens at end of combat.)

Temporal Mastery

Take an extra turn after this one. Exile Temporal Mastery.
Miracle {1}{U} (You may cast this card for its miracle cost when you draw it if it's the first card you drew this turn.)

Expropriate

Council's dilemma — Starting with you, each player votes for time or money. For each time vote, take an extra turn after this one. For each money vote, choose a permanent owned by the voter and gain control of it. Exile Expropriate.

The Ninth Doctor

Haste
Into the TARDIS — Whenever The Ninth Doctor becomes untapped during your untap step, you get an additional upkeep step after this step.

Sibylline Soothsayer

Temporal Foresight — When Sibylline Soothsayer enters, reveal cards from the top of your library until you reveal a nonland card with mana value 3 or greater. Exile that card with three time counters on it. If it doesn't have suspend, it gains suspend. Put the rest of the revealed cards on the bottom of your library in a random order.

Ancient Brass Dragon

Flying
Whenever Ancient Brass Dragon deals combat damage to a player, roll a d20. When you do, put any number of target creature cards with total mana value X or less from graveyards onto the battlefield under your control, where X is the result.

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.)

Alrund's Epiphany

Create two 1/1 blue Bird creature tokens with flying. Take an extra turn after this one. Exile Alrund's Epiphany.
Foretell {4}{U}{U} (During your turn, you may pay {2} and exile this card from your hand face down. Cast it on a later turn for its foretell cost.)

Ecstatic Beauty

Exile the top three cards of your library. You may play those cards until end of turn. Put four time counters on each of those cards that has suspend.
Suspend 4—{R}

Walk the Aeons

Buyback—Sacrifice three Islands. (You may sacrifice three Islands in addition to any other costs as you cast this spell. If you do, put this card into your hand as it resolves.)
Target player takes an extra turn after this one.

Ulamog, the Ceaseless Hunger

When you cast this spell, exile two target permanents.
Indestructible
Whenever Ulamog, the Ceaseless Hunger attacks, defending player exiles the top twenty cards of their library.

Spark Double

You may have Spark Double enter as a copy of a creature or planeswalker you control, except it enters with an additional +1/+1 counter on it if it's a creature, it enters with an additional loyalty counter on it if it's a planeswalker, and it isn't legendary.

Passionate Archaeologist

Commander creatures you own have "Whenever you cast a spell from exile, this creature deals damage equal to that spell's mana value to target opponent."

Amy Pond

Partner with Rory Williams (When this creature enters, 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.)

Killer

Killer deals 3 damage to target creature and each other creature that shares a creature type with it.

Coward

Target creature can't block this turn and becomes a Coward in addition to its other types until end of turn.
Time travel.

Coward // Killer

Time Beetle

Skulk (This creature can't be blocked by creatures with greater power.)
Parallel Universe — Whenever Time Beetle deals combat damage to a player, time travel. (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.)

Talisman of Creativity

{T}: Add {C}.
{T}: Add {U} or {R}. Talisman of Creativity deals 1 damage to you.

Sakashima of a Thousand Faces

You may have Sakashima of a Thousand Faces enter as a copy of another creature you control, except it has Sakashima of a Thousand Faces's other abilities.
The "legend rule" doesn't apply to permanents you control.
Partner (You can have two commanders if both have partner.)

Beacon of Tomorrows

Target player takes an extra turn after this one. Shuffle Beacon of Tomorrows into its owner's library.

Rise of the Eldrazi

This spell can't be countered.
Destroy target permanent. Target player draws four cards. Take an extra turn after this one.
Exile Rise of the Eldrazi.

Quantum Misalignment

Create a token that's a copy of target creature you control, except it isn't legendary.
Rebound (If you cast this spell from your hand, exile it as it resolves. At the beginning of your next upkeep, you may cast this card from exile without paying its mana cost.)

Time Warp

Target player takes an extra turn after this one.

Irenicus's Vile Duplication

Create a token that's a copy of target creature you control, except the token has flying and it isn't legendary.

Temporal Manipulation

Sinister Concierge

When Sinister Concierge dies, you may exile it and put three time counters on it. If you do, exile up to one target creature and put three time counters on it. Each card exiled this way that doesn't have suspend gains suspend. (For each card with suspend, its owner removes a time counter from it at the beginning of their upkeep. When the last is removed, they may cast it without paying its mana cost. Those creature spells have haste.)

Part the Waterveil

Take an extra turn after this one. Exile Part the Waterveil.
Awaken 6—{6}{U}{U}{U} (If you cast this spell for {6}{U}{U}{U}, also put six +1/+1 counters on target land you control and it becomes a 0/0 Elemental creature with haste. It's still a land.)

Nexus of Fate

Take an extra turn after this one.
If Nexus of Fate would be put into a graveyard from anywhere, reveal Nexus of Fate and shuffle it into its owner's library instead.

Time Stretch

Target player takes two extra turns after this one.

Sol Ring

Mox Tantalite

Suspend 3—{0} (Rather than cast this card from your hand, pay {0} and exile it with three time counters on it. At the beginning of your upkeep, remove a time counter. When the last is removed, you may cast it without paying its mana cost.)
{T}: Add one mana of any color.

Reality Strobe

Return target permanent to its owner's hand. Exile Reality Strobe with three time counters on it.
Suspend 3—{2}{U} (Rather than cast this card from your hand, you may pay {2}{U} and exile it with three time counters on it. At the beginning of your upkeep, remove a time counter. When the last is removed, you may cast it without paying its mana cost.)

Vampiric Tutor

Search your library for a card, then shuffle and put that card on top. You lose 2 life.

Rousing Refrain

Add {R} for each card in target opponent's hand. Until end of turn, you don't lose this mana as steps and phases end. Exile Rousing Refrain with three time counters on it.
Suspend 3—{1}{R} (Rather than cast this card from your hand, you may pay {1}{R} and exile it with three time counters on it. At the beginning of your upkeep, remove a time counter. When the last is removed, you may cast it without paying its mana cost.)