Andy Matuschak (@andy_matuschak): A consistently valuable interface design prompt for me: how would I do [X activity] with paper/pen/physical tools? The answer is often so much more fluid and improvisational than typical UI idioms and "data structures" tend to produce!
If I "highlight" something on a computer, it needs to represent that with a literal start offset and length. But annotating a physical document is often intentionally vague and gestural—attach a sticky to the general vicinity of an area, shade a line down the margin, etc.
I can improvise purpose-specific solutions with a physical highlighter: draw a box around something; make special marks in a personal code; write big-font marginalia. Most interfaces permit only pre-set verbs and a small surrounding space of creative repurposing.
This is an old problem, of course. There's a great discussion in "Formality considered harmful"[1] (via @JoelChan86, I think!). See also Smalltalk, Dynamicland, Chalktalk…
[1] http://andymatuschak.org/files/papers/Shipman%20and%20Marshall%20-%201999%20-%20Formality%20Considered%20Harmful%20Experiences,%20Emergin.pdf