Ferropede

Ferropede can't be blocked.
Whenever Ferropede deals combat damage to a player, you may 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.

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.)

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.

Vampire Hexmage

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

Medicine Runner

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

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.

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.