Kaldra Compleat

Living weapon
Indestructible
Equipped creature gets +5/+5 and has first strike, trample, indestructible, haste, and "Whenever this creature deals combat damage to a creature, exile that creature."
Equip {7}

Colossus of Akros

Defender, indestructible
{10}: Monstrosity 10. (If this creature isn't monstrous, put ten +1/+1 counters on it and it becomes monstrous.)
As long as Colossus of Akros is monstrous, it has trample and can attack as though it didn't have defender.

Hammer of Nazahn

Whenever Hammer of Nazahn or another Equipment you control enters, you may attach that Equipment to target creature you control.
Equipped creature gets +2/+0 and has indestructible.
Equip {4}

Kodama of the East Tree

Reach
Whenever another permanent you control enters, if it wasn't put onto the battlefield with this ability, you may put a permanent card with equal or lesser mana value from your hand onto the battlefield.
Partner (You can have two commanders if both have partner.)

Ghost of Ramirez DePietro

Ghost of Ramirez DePietro can't be blocked by creatures with toughness 3 or greater.
Whenever Ghost of Ramirez DePietro deals combat damage to a player, choose up to one target card in a graveyard that was discarded or put there from a library this turn. Put that card into its owner's hand.
Partner (You can have two commanders if both have partner.)

Creepy Doll

Indestructible
Whenever Creepy Doll deals combat damage to a creature, flip a coin. If you win the flip, destroy that creature.

Harmonious Emergence

Enchant land you control
Enchanted land is a 4/5 green Spirit creature with vigilance and haste. It's still a land.
If enchanted land would be destroyed, instead sacrifice Harmonious Emergence and that land gains indestructible until end of turn.

Grappling Sundew

Defender, reach
{4}{G}: Grappling Sundew gains indestructible until end of turn. (Damage and effects that say "destroy" don't destroy this creature.)

Darksteel Forge

Artifacts you control have indestructible. (Effects that say "destroy" don't destroy them. Artifact creatures with indestructible can't be destroyed by damage.)

Eldrazi Monument

Creatures you control get +1/+1 and have flying and indestructible.
At the beginning of your upkeep, sacrifice a creature. If you can't, sacrifice Eldrazi Monument.

Impervious Greatwurm

Convoke (Your creatures can help cast this spell. Each creature you tap while casting this spell pays for {1} or one mana of that creature's color.)
Indestructible

Amaranthine Wall

Defender
{2}: Amaranthine Wall gains indestructible until end of turn. (Damage and effects that say "destroy" don't destroy it.)

Heroic Intervention

Permanents you control gain hexproof and indestructible until end of turn.

Darksteel Plate

Indestructible
Equipped creature has indestructible.
Equip {2}

Majestic Myriarch

Majestic Myriarch's power and toughness are each equal to twice the number of creatures you control.
At the beginning of each combat, Majestic Myriarch gains flying until end of turn if you control a creature with flying. The same is true for first strike, double strike, deathtouch, haste, hexproof, indestructible, lifelink, menace, reach, trample, and vigilance.

Koma, Cosmos Serpent

This spell can't be countered.
At the beginning of each upkeep, create a 3/3 blue Serpent creature token named Koma's Coil.
Sacrifice another Serpent: Choose one —
• Tap target permanent. Its activated abilities can't be activated this turn.
• Koma, Cosmos Serpent gains indestructible until end of turn.