In general, I think Pacifism effects (especially ones that delete rules text à la Darksteel Mutation) are underused. You can just Sun Titan them on to a creature with shroud or hexproof.
I've been preferring "remain on the battlefield" removal over the years as well - trading in my Rapid Hybridizations and Pongifys for things like Ice Cage, Lost in Thought, and Deep Freeze, which are criminally underplayed, IMO. Claustrophobia and Waterknot are effective in aggro-heavy meta (and Narcolepsy to come extent if the creature doesn't also have a tapping activated ability). Hitting a commander, particularly in the early game (or even the right timing mid- or late-game) can often effectively shut down an opponent. Sure, they let the creature remain a creature (unlike the even more permanent-ish Imprisoned in the Moon, which is not underplayed removal), so a board wipe gives them a chance to get the creature back somehow from either the yard or command zone, but then that's still one more step the opponent has to think about or hoop they have to jump through to get access to that card again, and I've found that these can sometimes be board wipe deterrents and other opponents wouldn't likely want that player to have their commander or other dangerous "thing" back again.
Lost in Thought has been particularly effective, at least in my meta.
Lignify. There isn't a lot of this effect in green, but turning problematic commanders into 0/4 treefolk never ceases to amuse me and not a lot of colors run enchantment removal.
WBG Karador, Ghost Chieftain
B Toshiro Umezawa
BG Pharika, God of Affliction - Necromancy and Politics
WWW The Church of Heliod
WBR Zurgo, Helmsmasher
RG Wort, the Raidmother
UBR Jeleva, Nephalia's Scourge
UG Vorel of the Hull Clade
I've been preferring "remain on the battlefield" removal over the years as well - trading in my Rapid Hybridizations and Pongifys for things like Ice Cage, Lost in Thought, and Deep Freeze, which are criminally underplayed, IMO. Claustrophobia and Waterknot are effective in aggro-heavy meta (and Narcolepsy to come extent if the creature doesn't also have a tapping activated ability). Hitting a commander, particularly in the early game (or even the right timing mid- or late-game) can often effectively shut down an opponent. Sure, they let the creature remain a creature (unlike the even more permanent-ish Imprisoned in the Moon, which is not underplayed removal), so a board wipe gives them a chance to get the creature back somehow from either the yard or command zone, but then that's still one more step the opponent has to think about or hoop they have to jump through to get access to that card again, and I've found that these can sometimes be board wipe deterrents and other opponents wouldn't likely want that player to have their commander or other dangerous "thing" back again.
Lost in Thought has been particularly effective, at least in my meta.
Current EDH
UThassa, God of the Sea devotion control
WRGTana, the Bloodsower & Sidar Kondo of Jamuraa partners weenie tokens
UUnesh, Criosphinx Sovereign Sphinx tribal
WUTaigam, Ojutai Master tokens on the rebound spellslinger
GRhonas the Indomitable green creature beats
UGRashmi, Eternities Crafter ETB tribal
Retired EDH
WURGKynaios and Tiro of Meletis group hug
URThe Locust God draw swarm
UTalrand, Sky Summoner funsies blue spells
WBObzedat, Ghost Council life gain/drain
Pioneer:UR Pheonix
Modern:U Mono U Tron
EDH
GB Glissa, the traitor: Army of Cans
UW Dragonlord Ojutai: Dragonlord NOjutai
UWGDerevi, Empyrial Tactician "you cannot fight the storm"
R Zirilan of the claw. The solution to every problem is dragons
UB Etrata, the Silencer Cloning assassination
Peasant cube: Cards I own
Credit to DolZero for this awesome sig!