The Note to Rachel lies on a table in the house with the banging door in Bill's Town. After you get the bow and cross the rooftops, enter the room with the infected; the note is under a wall where Rachel's name is painted with an arrow.
Ezra writes in a hurry as soldiers go door to door putting people on buses. He could not reach Rachel, has packed their things into suitcases and promises to wait for her in the quarantine zone.
Ellie reads Rachel's name aloud as she passes, and after the note she asks whether the two ever found each other. Joel has no idea, but Ellie chooses to believe they did.
Bill's Map
Bill's Map is Bill's hand-annotated map of Lincoln, on a table with an engine near the door you come in through at his safehouse, right after you meet him.
Bombs Note
The Bombs Note is on a table to the left in the side room off the nave of Bill's church. Go into the room on the right, the one Bill makes clear is not the confessional.
Boy's Diary
The Boy's Diary is on the windowsill of a child's bedroom painted with stripes and cars, upstairs in the second house with the dry pool in the new territory beyond the church graveyard.
Fences Note
The Fences Note is another of Bill's reminders, on the table in the back room of his safehouse near the pipe he handcuffs Ellie to.