Okay, the voices in my head made me research all this paper-related stuff some more.
Clipboards: The metal ones appeared at least twice in each pilot (one can be spotted on Delta Vega), then were promptly obsolesced by the debut of the electronic Feinberger version in Corbomite.
Books: I found an additional book in Balance of Terror, on the Chapel podium, as well as a stack of books in the second pilot's rec room. (Also note in Court Martial that Cogley appears to write on something that looks like a manila folder.)
Books are also pretty common in various crew quarters (the following examples are not exhaustive).
Below I have compiled everyone's contributions, but I did not have the patience to track down every example of books in crew quarters.
| 0x00 Cage | papers/clipboard | Pike's quarters; clipboard is metal/non-electronic |
| 0x00 Cage | printout | of SS Columbia's distress call, from printer on bridge |
| 0x00 Cage | papers/clipboard | on the bridge; clipboard is metal/non-electronic |
| 1x01 WNMHGB | books | in rec room |
| 1x01 WNMHGB | medical records | (and ESP ratings) of Mitchell & Dehner, digitized & written on |
| 1x01 WNMHGB | documents | digitized & read by Mitchell in sickbay |
| 1x01 WNMHGB | papers/clipboard | metal clipboard; on table in briefing room |
| 1x08 Balance | book | on podium in chapel for wedding |
| 1x08 Balance | book | Table of Comets |
| 1x09 What Are | cardstock/paper | in Kirk's command pack, stolen by android duplicate |
| 1x12 Conscience | scripts | in Karidian's quarters; two; probably Macbeth and Hamlet |
| 1x12 Conscience | paper | Kodos speech quotation brought to Karidian by Kirk |
| 1x12 Conscience | printouts | Kodos vs. Karidian voice prints |
| 1x14 Court | deposition | Kirk checks his sworn statement in Stone's office |
| 1x14 Court | books (& folder?) | Samuel T. Cogley's substantial collection |
| 1x15 Menagerie | book/file/dossier | Starfleet's top secret file on Talos IV |
| 1x27 Errand | proclamation | Kor's proclamation to the Organians |
| 1x01-09 | labels | tiny white paper labels on microtapes |
| 1x02,03,06; 2x04,07 | cardstock | Jeppesen flight computers (cardstock with a little plastic) |
| multiple episodes | books | in various crew quarters |
As an addendum, I'm listing separately the items that seem to belong to such an earlier time period that they feel different from the examples above. I recognize there are some judgement calls here; some might prefer Cogley's books to move down here, or Flint's most recent manuscript(s) to move up. I guess I gave extra weight to Cogley since he's still an active part of Federation society.
| 2x20 Piece | book | Chicago Mobs of the Twenties (1992) |
| 2x26 Assignment | typewriter w/paper | Gary Seven's auto-transcribing typewriter (1960s Earth) |
| 3x21 Requiem | manuscripts | Flint's musical compositions (don't know how old they are) |
Nearly all images sourced from TrekCore, chopped down by me; I think one or two may have come from P+, especially in the bookshelf montage.