Ensnared by the Mara

Each opponent faces a villainous choice — They exile cards from the top of their library until they exile a nonland card, then you may cast that card without paying its mana cost, or that player exiles the top four cards of their library and Ensnared by the Mara deals damage equal to the total mana value of those exiled cards to that player.

The War Doctor

Whenever one or more other permanents phase out and whenever one or more other cards are put into exile from anywhere, put a time counter on The War Doctor.
Whenever The War Doctor attacks, it deals damage equal to the number of time counters on it to any target. If a creature dealt damage this way would die this turn, exile it instead.

Lion Sash

{W}: Exile target card from a graveyard. If it was a permanent card, put a +1/+1 counter on Lion Sash.
Equipped creature gets +1/+1 for each +1/+1 counter on Lion Sash.
Reconfigure {2} ({2}: Attach to target creature you control; or unattach from a creature. Reconfigure only as a sorcery. While attached, this isn't a creature.)

Path to Exile

Exile target creature. Its controller may search their library for a basic land card, put that card onto the battlefield tapped, then shuffle.

Swords to Plowshares

Exile target creature. Its controller gains life equal to its power.

Lae'zel, Vlaakith's Champion

If you would put one or more counters on a creature or planeswalker you control or on yourself, put that many plus one of each of those kinds of counters on that permanent or player instead.
Choose a Background (You can have a Background as a second commander.)

Swiftfoot Boots

Equipped creature has hexproof and haste. (It can't be the target of spells or abilities your opponents control.)
Equip {1}

Lightning Greaves

Equipped creature has haste and shroud. (It can't be the target of spells or abilities.)
Equip {0}

Dance with Calamity

Shuffle your library. As many times as you choose, you may exile the top card of your library. If the total mana value of the cards exiled this way is 13 or less, you may cast any number of spells from among those cards without paying their mana costs.

No More

Any number of target creatures you control phase out.
Fuse (You may cast one or both halves of this card from your hand.)

Gallifrey Falls

Gallifrey Falls deals 4 damage to each creature. If a creature dealt damage this way would die this turn, exile it instead.
Fuse (You may cast one or both halves of this card from your hand.)

Gallifrey Falls // No More

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.)

Valakut Exploration

Landfall — Whenever a land enters the battlefield under your control, exile the top card of your library. You may play that card for as long as it remains exiled.
At the beginning of your end step, if there are cards exiled with Valakut Exploration, put them into their owner's graveyard, then Valakut Exploration deals that much damage to each opponent.

Into the Time Vortex

Cascade (When you cast this spell, exile cards from the top of your library until you exile a nonland card that costs less. You may cast it without paying its mana cost. Put the exiled cards on the bottom in a random order.)
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.)

Guardian of Faith

Flash
Vigilance
When Guardian of Faith enters the battlefield, any number of other target creatures you control phase out. (Treat them and anything attached to them as though they don't exist until their controller's next turn.)

Professional Face-Breaker

Menace
Whenever one or more creatures you control deal combat damage to a player, create a Treasure token.
Sacrifice a Treasure: Exile the top card of your library. You may play that card this turn.

Tavern Brawler

Commander creatures you own have "At the beginning of your upkeep, exile the top card of your library. This creature gets +X/+0 until end of turn, where X is that card's mana value. You may play that card this turn."

Guff Rewrites History

For each player, choose target nonenchantment, nonland permanent that player controls. Those permanents' owners shuffle them into their libraries. Each player who controlled one of those permanents exiles cards from the top of their library until they exile a nonland card, then puts the rest on the bottom of their library in a random order. Each player may cast the nonland card they exiled without paying its mana cost.

Ryan Sinclair

Whenever Ryan attacks, exile cards from the top of your library until you exile a nonland card. You may cast the exiled card without paying its mana cost if it's a spell with mana value less than or equal to Ryan's power. Put the exiled cards not cast this way on the bottom of your library in a random order.
Doctor's companion (You can have two commanders if the other is the Doctor.)

TARDIS

Flying
Whenever TARDIS attacks, if you control a Time Lord, the next spell you cast this turn has cascade and you may planeswalk.
Crew 2 (Tap any number of creatures you control with total power 2 or more: This Vehicle becomes an artifact creature until end of turn.)

Four Knocks

Vanishing 4 (This enchantment enters the battlefield with four time counters on it. At the beginning of your upkeep, remove a time counter from it. When the last is removed, sacrifice it.)
At the beginning of your precombat main phase, draw a card.

Laelia, the Blade Reforged

Haste
Whenever Laelia, the Blade Reforged attacks, exile the top card of your library. You may play that card this turn.
Whenever one or more cards are put into exile from your library and/or your graveyard, put a +1/+1 counter on Laelia.

The Moment

At the beginning of your upkeep, put a time counter on The Moment.
{2}, {T}: Untap target creature you control. It phases out until The Moment leaves the battlefield.
{3}, {T}: Destroy each nonland permanent with mana value less than or equal to the number of time counters on The Moment. Then sacrifice The Moment. Activate only as a sorcery.

The Pandorica

You may choose not to untap The Pandorica during your untap step.
{1}{W}, {T}: Untap another target nonland permanent, then it phases out. It can't phase in for as long as The Pandorica remains tapped. When The Pandorica becomes untapped or leaves the battlefield, that permanent phases in. Activate only as a sorcery.

The Flux

(As this Saga enters and after your draw step, add a lore counter. Sacrifice after VI.)
I — The Flux deals 4 damage to target creature an opponent controls.
II, III, IV, V — Exile the top card of your library. You may play that card this turn.
VI — Add six {R}.

The Day of the Doctor

(As this Saga enters and after your draw step, add a lore counter. Sacrifice after IV.)
I, II, III — Exile cards from the top of your library until you exile a legendary card. You may play that card for as long as The Day of the Doctor remains on the battlefield. Put the rest of those exiled cards on the bottom of your library in a random order.
IV — Choose up to three Doctors. You may exile all other creatures. If you do, The Day of the Doctor deals 13 damage to you.

Grasp of Fate

When Grasp of Fate enters the battlefield, for each opponent, exile up to one target nonland permanent that player controls until Grasp of Fate leaves the battlefield. (Those permanents return under their owners' control.)

Robe of Stars

Equipped creature gets +0/+3.
Astral Projection — {1}{W}: Equipped creature phases out. (Treat it and anything attached to it as though they don't exist until its controller's next turn.)
Equip {1}

The Ozolith

Whenever a creature you control leaves the battlefield, if it had counters on it, put those counters on The Ozolith.
At the beginning of combat on your turn, if The Ozolith has counters on it, you may move all counters from The Ozolith onto target creature.

The Wedding of River Song

Draw two cards, then you may exile a nonland card from your hand with a number of time counters on it equal to its mana value. Then target opponent does the same. Cards exiled this way that don't have suspend gain suspend.
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.)