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
- Lab Scale
- 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.