What unique items could become unobtainable?

fallout-4

After finishing The Human Error quest with the resolution that made it impossible to buy the unique equipment from Penny Fitzgerald (Destroyer's Helmet and Justice), I realized there must be unique gear that can become unobtainable after certain quests/events if not previously obtained.

I also know there is a point later in the main story quest line that will make you an enemy of some factions, which probably leads to more unobtainable gear if they aren't purchased/obtained before the respective quest is complete.

Is there a list of gear that can become unobtainable, and the quest/event that makes it unobtainable? I'd hate to find out down the line that I missed desirable unique equipment by unknowingly progressing through a quest.

There are a variety of weapons available from both side quests and faction quests, depending on your allegiances in the game and how thoroughly you clear out the side quests it's quite easy to miss many. This list doesn't include weapons you may find as a result of murdering friendlies (for example killing Virgil to get Virgil's rifle).

Side quests

Below is the list of items directly available as a result of quests:

Agatha’s Dress, reward for completing Curtain Call as a female
Ashmaker Minigun, potential reward for completing Big Dig
Broadsider, potential reward for completing Last Voyage of the USS Constitution
Captain Ironsides’ Hat, potential reward for completing Last Voyage of the USS Constitution
Eddie's Peace .44 Pistol, found during the quest Long Time Coming
Lorenzo's Artifact Gamma Gun, reward for completing The Secret of Cabot House
Reba II Hunting Rifle, potential reward for completing Barney Rock
Reginald’s Suit, reward for completing Curtain Call as a male
Shem Drowne Sword, reward for completing The Gilded Grasshopper
Silver Shroud Armor, reward for completing The Silver Shroud
Silver Shroud Hat, reward for completing The Silver Shroud
Silver Submachine Gun, reward for completing The Silver Shroud

In addition to the above list, there are a variety of instances throughout the game where as a result of your actions a NPC vendor will become hostile to you. Such examples include the Battle of Bunker Hill resulting in the deaths of vendor NPCs like Deb, and Human Error resulting in the citizens of Covenant becoming hostile you, like Penny Fitzgerald. I'm not going to include Diamond City or Goodneighbor in this list because if you become hostile to them that's your own fault!

Sold by Deb in Bunker Hill

Destroyer's left arm
Black Ops Chestpiece
Black Ops Right Shinguard

Sold by Penny in Covenant

Destroyer's helmet

Brotherhood of Steel quests

With the exception of Righteous Authority, all of the weapons below require progression through the Brotherhood of Steel quest line to the point where you have access to the Prydwen, and then some more require you to hold a particular rank within the Brotherhood.

Needless to say, if you become hostile to the Brotherhood of Steel you will lose access to this faction's vendors.

AX90 Fury Plasma Rifle, sold on the Prydwen
Exemplar’s T-60c Torso, reward for completing Duty of Dishonor by persuading Clarke to turn himself in
Righteous Authority Laser Rifle, quest reward for completing Call to Arms
Steadfast BOS Combat Armor Chest Piece, potential quest reward for completing The Lost Patrol
Survivor's Special Laser Rifle, potential quest reward for completing The Lost Patrol
Visionary’s T-60c Helm, for completing A Loose End

Requisitioned from Teagan

Commando Chest Piece
Commando Helmet
Death From Above Missile Launcher, sold by Teagan after reaching the rank of Paladin
Honor
Sentinel's Plasmacaster Plasma Thrower, sold by Teagan on the Prydwen after reaching the rank of Sentinel
Vengeance

Minutemen quests

The Minutemen don't really have anything all that special, certainly not before taking back the Castle but then you do get access to a Gauss Rifle...

The Last Minute Gauss Rifle, sold at the Castle after completing Old Guns from Ronnie

Railroad quests

I haven't included the Railway Rifle in this list as it is possible to find this elsewhere, but the Railway Rifle can be a possible quest reward for completing Underground Undercover. Failing that you can head over to Big John's Salvage for a guaranteed spawn.

Needless to say, if you become hostile to the Railroad you will lose access to this faction's vendors.

Deliverer 10mm Pistol, reward for completing Tradecraft
Final Judgement Gatling Laser, carried by Elder Maxson during Precipice of War
Tinker Tom Special Hunting Rifle, sold by Tinker Tom in the Railroad HQ

Institute quests

The super powerful Experiment 18A is available very early on in the Institute quest line, you can pick it up immediately after speaking to each of the department heads before you first leave the Institute. The Wazer Wifle is an end game weapon only available after completing three unmarked quests to fetch items from the wasteland.

Needless to say, if you become hostile to the Institute you will lose access to this faction's vendors.