Is there any scrappable junk I should hold on to that could otherwise be used for other purposes?
There are many scrappable junk items that can be used whole for other purposes, for instance for specific quests or as a crafting ingredient:
Used for Quests (repeatable quests italicized)
- A Biometric Scanner and a Military-Grade Circuit Board are required for the main quest The Molecular Level.
- 4 High-Powered Magnets are needed for the Brotherhood of Steel quest Liberty Reprimed, but they are provided in the Boston Airport workshop.
- Yellow and Blue paint cans - Abbot (Diamond City)
- Bloatfly Gland - Doctor Duff (Diamond City)
- Bag of Fertilizer - Priscilla Penske (Vault 81)
- Adjustable Wrench, Ball-peen Hammer, Combination Wrench, Hammer, Screwdriver, Wrench - Calvin (Vault 81)
- Anti-Freeze Bottle, Gas Canister (for Reactor Coolant) - Proctor Ingram (Prydwen)
Used as Crafting Ingredients
- Abraxo Cleaner - Mentats, Mind Cloud Syringe
- Anti-Freeze Bottle - Berry Mentats, Berserk Syringe, Yellow Belly Syringe
- Baseball - Baseball Grenade
- Bloatfly Gland - Bloatfly Larva Syringe
- Bloodsac - Skeeto Spit
- Brahmin Skull - Mounted Brahmin Skull
- Coffee Tin - Slocum's BuzzBites
- Molerat Teeth - Mounted Molerat Skull
- Pencil - Endangerol Syringe
- Radscropion Stinger - Radscorpion Venom Syringe
- Skull - Spiked Pole
The big one that I try to avoid scrapping is Pre War Money.
Cloth is easy to come by, and Pre-War Money has a high resale value and zero weight, which makes it an ideal way to pull caps out of an ATM machine trade with merchants for a few extra caps whenever you come across one.