What items look like scrappable junk, but can't be scrapped?

To my knowledge, all the items that seem like junk, but are not scrappable, appear in the 'Misc' section of your inventory instead of the 'Junk' tab. You might have noticed that when collecting folders, for example, they sit in the 'Misc' tab of your Pip-Boy inventory until you remove them yourself, and do not move when performing the "store all junk" action at a workshop.

That being said, the most complete list I've been able to find is at the Fallout 4 Wiki article on Miscellaneous Items, more specifically the "Other Items" section. This section contains all of the items I've run across that seem like junk, but was unable to scrap:

• Bobby Pin
• Book Return Token/Overdue book
• Burnt Book/Textbook
• Burnt Fashion/Lifestyle/Trade Magazines
• Burnt Grognak/Manta-Man/Unstoppables Comics
• Cybernetic Limb Actuator
• Cybernetic Pain Inhibitor
• Delivered Boston Bugle
• Eyebot/Mr. Handy/Mr. Gutsy/Protectron/Robot Parts/Sentry Bot Models
• Folder
• Lab Scale
• Napkin
• Stingwing Barb
• Subway Token
• Vault-Tec Lunchbox

Some items in this list, while not scrappable, still serve some purpose for crafting or gameplay. Stingwing barbs and Vault-Tec lunchboxes are used in crafting. Bobby pins are, of course, for lockpicking. Overdue books/book return tokens are used at Book Return terminals, and Subway Tokens are for paying Subway Stewards.

Furthermore, not all of these items are weightless. Whereas collecting all folders might add some clutter to your inventory, collecting burnt books/textbooks also has the negative effect of adding 1 weight each (with a value of 0), so should be avoided to prevent being over-encumbered.

Needless to say, other items that appear in the 'Misc' inventory tab, such as holotapes, notes, quest items, etc., cannot be scrapped. The one exception to this seems to be the RFID Device, given to you during the quest "Jackpot". It is not marked as a quest item, which would prevent it from being scrapped.

Your inventory is broken into several categories:

• Weapons
• Apparel
• Aid
• Misc
• Junk
• Mods
• Ammo

Categories in bold are the ones which contain items which are generally easy to break down into scrap. All non-legendary Weapons can be broken down manually at a workbench. Most non-legendary armor in the Apparel category can be broken down manually at a workbench as well, but not all Apparel is armor and there's even some exceptions which are armor. All Junk will be automatically be broken down as needed during crafting.

Workstations also have a somewhat-hidden inventory of items that can be used in settlement construction, which the player has either built or collected and chosen to put into storage there. When not labeled as critical for a mission, these items can be scrapped in construction mode after you place them in the environment.

It's conceivable that some Aid/Misc/Mods/Ammo items (and non-armor Apparel) could be scrapped if they were dropped in the environment and then viewed in construction mode. However, I have not thoroughly tested this myself and I personally consider it to be generally unlikely. (Maybe the non-armor Apparel will go, but probably not the rest.)

At the very least, I do know that most - if not all - food items (which would be collected under Aid) cannot be scrapped. I find it generally annoying since it just adds a bit more hassle to cleanup of things like Blamco Mac & Cheese whenever I'm taking over a new settlement.