One time

Vampire Hexmage

First strike
Sacrifice Vampire Hexmage: Remove all counters from target permanent.

Reuseable

Hex Parasite

{X}{B/P}: Remove up to X counters from target permanent. For each counter removed this way, Hex Parasite gets +1/+0 until end of turn. ({B/P} can be paid with either {B} or 2 life.)

Unuseable

Tayam, Luminous Enigma

Each other creature you control enters with an additional vigilance counter on it.
{3}, Remove three counters from among creatures you control: Mill three cards, then return a permanent card with mana value 3 or less from your graveyard to the battlefield.

Nesting Grounds

{T}: Add {C}.
{1}, {T}: Move a counter from target permanent you control onto another target permanent. Activate only as a sorcery.

Thief of Blood

Flying
As Thief of Blood enters, remove all counters from all permanents. Thief of Blood enters with a +1/+1 counter on it for each counter removed this way.

Medicine Runner

When Medicine Runner enters, you may remove a counter from target permanent.

Fain, the Broker

{T}, Sacrifice a creature: Put two +1/+1 counters on target creature.
{T}, Remove a counter from a creature you control: Create a Treasure token.
{T}, Sacrifice an artifact: Create a 2/1 white and black Inkling creature token with flying.
{3}{B}: Untap Fain, the Broker.

Somewhat Useful

Clockspinning

Buyback {3} (You may pay an additional {3} as you cast this spell. If you do, put this card into your hand as it resolves.)
Choose a counter on target permanent or suspended card. Remove that counter from that permanent or card or put another of those counters on it.

Spinal Parasite

Sunburst (This enters with a +1/+1 counter on it for each color of mana spent to cast it.)
Remove two +1/+1 counters from Spinal Parasite: Remove a counter from target permanent.

Thrull Parasite

Extort (Whenever you cast a spell, you may pay {W/B}. If you do, each opponent loses 1 life and you gain that much life.)
{T}, Pay 2 life: Remove a counter from target nonland permanent.

Thornmantle Striker

When Thornmantle Striker enters, choose one —
• Remove X counters from target permanent, where X is the number of Elves you control.
• Target creature an opponent controls gets -X/-X until end of turn, where X is the number of Elves you control.

Scholar of New Horizons

Scholar of New Horizons enters with a +1/+1 counter on it.
{T}, Remove a counter from a permanent you control: Search your library for a Plains card and reveal it. If an opponent controls more lands than you, you may put that card onto the battlefield tapped. If you don't put the card onto the battlefield, put it into your hand. Then shuffle.

Hexavus

Flying
Hexavus enters with six +1/+1 counters on it.
{1}, Remove a +1/+1 counter from Hexavus: Put a flying counter on another target creature.
{1}, Remove a counter from another creature you control: Put a +1/+1 counter on Hexavus.

Dramatist's Puppet

When Dramatist's Puppet enters, for each kind of counter on target permanent, put another counter of that kind on it or remove one from it.

Sanctuary Warden

Flying
Sanctuary Warden enters with two shield counters on it.
Whenever Sanctuary Warden enters or attacks, you may remove a counter from a creature or planeswalker you control. If you do, draw a card and create a 1/1 green and white Citizen creature token.

Ferropede

Ferropede can't be blocked.
Whenever Ferropede deals combat damage to a player, you may remove a counter from target permanent.

Quarry Hauler

When Quarry Hauler enters, for each kind of counter on target permanent, put another counter of that kind on it or remove one from it.

Price of Betrayal

Remove up to five counters from target artifact, creature, planeswalker, or opponent.

Soul Diviner

{T}, Remove a counter from an artifact, creature, land, or planeswalker you control: Draw a card.

Chisei, Heart of Oceans

Flying
At the beginning of your upkeep, sacrifice Chisei, Heart of Oceans unless you remove a counter from a permanent you control.

Power Conduit

{T}, Remove a counter from a permanent you control: Choose one —
• Put a charge counter on target artifact.
• Put a +1/+1 counter on target creature.

Heartless Act

Choose one —
• Destroy target creature with no counters on it.
• Remove up to three counters from target creature.

Resourceful Defense

Whenever a permanent you control leaves the battlefield, if it had counters on it, put those counters on target permanent you control.
{4}{W}: Move any number of counters from target permanent you control to another target permanent you control.

Leech Bonder

Leech Bonder enters with two -1/-1 counters on it.
{U}, {Q}: Move a counter from target creature onto a second target creature. ({Q} is the untap symbol.)