I couldn't sleep until 3 AM(in here) and UnlikeClockwork's post in General Discussion made me write this.
Before you start reading this, check here first.
I do not know what are retiring or going to be updated with Omega items.
I also didn't included unique medal/ring related. Only slot 1-5 uniques.
That said, let's start!
Collection
Item Hunting
The Collector : http://marvelheroes.info/achievement/4/
Very Special Things : http://marvelheroes.info/achievement/5/
Uniques
All of them : http://marvelheroes.info/achievements/collection/uniques/#0-25-1-0
Crafting
Gear
Uniquely Upgradeable : http://marvelheroes.info/achievement/41/
Enemies
Adversaries
Aim to Misbehave : http://marvelheroes.info/achievement/47/
Breaking Walter White : http://marvelheroes.info/achievement/48/ Blue Omega box, which contains boss unique.
Doom Deathmatch : http://marvelheroes.info/achievement/55/
Go Ahead, Make My Day : http://marvelheroes.info/achievement/61/
Legacy of Kraven : http://marvelheroes.info/achievement/62/
My Own Wurst Enemy : http://marvelheroes.info/achievement/65/ This requires cart.
Ninja Vanish : http://marvelheroes.info/achievement/66/
Steak for Dinner : http://marvelheroes.info/achievement/67/
Symbiote Civil War : http://marvelheroes.info/achievement/69/
Thanks, Gaz! : http://marvelheroes.info/achievement/70/
The Leaper : http://marvelheroes.info/achievement/72/
The Ninja : http://marvelheroes.info/achievement/73/
Trask's Revenge : http://marvelheroes.info/achievement/76/
Takedowns
Target Acquired: All-Father Brevik : http://marvelheroes.info/achievement/119/
Target Acquired: All-Father Brevik II : http://marvelheroes.info/achievement/120/
Target Acquired: All-Father Brevik III : http://marvelheroes.info/achievement/121/
Target Acquired: Doctor Doom II : http://marvelheroes.info/achievement/123/
Target Acquired: Doctor Doom III : http://marvelheroes.info/achievement/124/
Target Acquired: Doctor Octopus : http://marvelheroes.info/achievement/125/
Target Acquired: Kingpin II : http://marvelheroes.info/achievement/129/
Target Acquired: Kraven : http://marvelheroes.info/achievement/130/
Target Acquired: Kurse II : http://marvelheroes.info/achievement/132/
Target Acquired: Madame Hydra : http://marvelheroes.info/achievement/134/
Target Acquired: Magneto II : http://marvelheroes.info/achievement/809/
Target Acquired: Man-Ape II : http://marvelheroes.info/achievement/137/
Target Acquired: Man-Ape III : http://marvelheroes.info/achievement/138/
Target Acquired: Mister Hyde II : http://marvelheroes.info/achievement/141/
Target Acquired: Mister Sinister : http://marvelheroes.info/achievement/142/
Target Acquired: MODOK II : http://marvelheroes.info/achievement/144/
Target Acquired: Red Skull II : http://marvelheroes.info/achievement/146/
Target Acquired: Red Skull III : http://marvelheroes.info/achievement/147/
Target Acquired: Shocker : http://marvelheroes.info/achievement/148/
Target Acquired: The Hood : http://marvelheroes.info/achievement/150/
Events
A.R.M.O.R. Incursion
New Set of A.R.M.O.R. : http://marvelheroes.info/achievement/839/
Game Modes
Hightown Patrol
Impostors Detected: War Skrulls : http://marvelheroes.info/achievement/971/
Impostors Detected: X-Men : http://marvelheroes.info/achievement/972/
Midtown Patrol
Need for Speed : http://marvelheroes.info/achievement/223/
Terminals
All in Doom's Time : http://marvelheroes.info/achievement/240/
Heroes
Besides each hero's "own all of XXX's unique items"
Black Widow
Warm Operator : http://marvelheroes.info/achievement/444/
Captain America
Independence Day : This is a secret achievement. Equip Iron Patriot Repulsors and /salute.
Daredevil
Shadowland : http://marvelheroes.info/achievement/483/
Doctor Strange
Iconoclasty : http://marvelheroes.info/achievement/506/
Ghost Rider
Johnny's Not Here Anymore : http://marvelheroes.info/achievement/527/
Green Goblin
Iron Patriot : http://marvelheroes.info/achievement/964/
Hawkeye
I Hope This Works : http://marvelheroes.info/achievement/535/
Shot through the heart... : http://marvelheroes.info/achievement/857/
Iron Man
Man Vs. Patriot : http://marvelheroes.info/achievement/575/
Punisher
Remember the Alamo : http://marvelheroes.info/achievement/664/
Spider-Man
Superior Revenge : http://marvelheroes.info/achievement/714/
Squirrel Girl
Need More Squirrels : http://marvelheroes.info/achievement/723/
War Machine
It Tested Well : http://marvelheroes.info/achievement/881/
Winter Soldier
Just Like Old Times : http://marvelheroes.info/achievement/785/
Wolverine
Let's Go, Bub : http://marvelheroes.info/achievement/795/
Oh, Canada : This is a secret achievement. Equip Guardian's Battle-suit and /cheer.
Planning Ahead : http://marvelheroes.info/achievement/863/
Miscellaneous
Advanced
My Bodyguard : http://marvelheroes.info/achievement/326/ tip : Do 75-100 enemies wave and DO NOT open chest, just keep stop bullying.
The Burning Crusade, Stage 3 : http://marvelheroes.info/achievement/329/
The Burning Crusade, Stage 7 : http://marvelheroes.info/achievement/333/
The Burning Crusade, Stage 9 : http://marvelheroes.info/achievement/335/
Raids
Muspelheim
Surtur Raid Uniques : http://marvelheroes.info/achievement/406/
Let me know if I missed something!