I don't have much of a "desk", so you'd have to unearth one of many baglike things.
Academic reading tends to be law review articles about copyrights, patents, privacy, telecom, etc: trying to keep up with the current state of areas I care about and would like to work in. Nonfiction is law/legal theory, economics, science, and "big think" type books. Some are trying to fix what I think are gaping holes in my education, some to have read what other people in my social circle are reading, some for pleasure, some for reference.
I usually keep more than one book open at a time. Right now I am reading Good Faith Collaboration, which is a new academic book about Wikipedia and its social structures; The Big Necessity for bathroom reading (because the thought of reading that as a bathroom book made me laugh); Guns, Germs, and Steel is on my nightstand (yes, I know, I'm a few years behind on that one...). I have The Gridlock Economy in my totebag because I was referencing it for a project; The Public Domain open in electronic form for the same reason.
Or you could take a glimpse through my LibraryThing: http://www.librarything.com/profile/mindspillage
Other things always present in my working space: pens, paper (don't ask me to do anything regarding math or logic without a writing implement in my hand), something to drink, remnants of craft supplies, something that plays music, something that tells time, something that will hold my hair out of my face, probably stray books of sheet music also. Things generally not present: a telephone or anything that makes unexpected noises.
Concerning "Guns, Germs, and Steel ": Murray Gell-Mann is involved in some interesting research on general patterns of civilization. But his and Diamond's schemes are just about some general and indirect indicators, not about what the essence of "civilization" is. To get an idea of that, I am curious about instances where "civilization" went down quickly. This puts e.g. "Berlin Diary: The Journal of a Foreign Correspondent 1934-1941", and "Human Smoke: The Beginnings of World War II, the End of Civilization" on my desk. A very remarkable case is told about in Simone Weil's "L'agonie d'une civilisation". I scanned two essay by Zbigniew Herbert on decivilization from this - someone curious to get them? "The Dream of Scipio" by Ian Pears sketches (in typical french history-through-novels manner) a thrilling pattern of several critical moments of the last 1500 years of European history.
What do I read?
On the internet, I read LW, the New York Times, and a Google feed of blogs. (Mostly math -- Terence Tao, Nuit Blanche, etc. -- but also Will Wilkinson and The American Scene on the political end, and The Geomblog for theoretical computer science.) When I need a cheerful pick-me-up I read BoingBoing. When I procrastinate I binge on The Atlantic or Yglesias or Reason, you know, the usual players in the news and commentary universe.
For school I read the predictable array of math textbooks. Most recently Caratheodory's book on conformal maps.
For pleasure reading -- normally I'm a literature person, but most recently I've just been going through Neal Stephenson books.
What's on my desk? Not a lot. File folders of papers, kleenex, desk lamp, notebook. My work (or "work") life is not very paper-intensive. My inbox? Now that's a mess.
Mostly math -- Terence Tao, Nuit Blanche, etc.
Can you unpack that etc.? I really enjoy Terence Tao's blog and would appreciate finding similar blogs.
Here's a list of math blogs. I don't read all of these myself, of course. What I actually try to keep up with, apart from Tao's blog:
Nuit Blanche, the blog of Igor Carron, which is about compressed sensing.
ChapterZero, written by a graduate student, mostly about random matrix theory.
Quomocodumque, written by Jordan Ellenberg, about nearly everything.
Three-Toed Sloth by Cosma Shalizi, who's a statistician, about statistics and lots of other subjects.
Here's a list of math blogs. I don't read all of these myself, of course. What I actually try to keep up with, apart from Tao's blog:
Nuit Blanche, the blog of Igor Carron, which is about compressed sensing.
ChapterZero, written by a graduate student, mostly about random matrix theory.
Quomocodumque, written by Jordan Ellenberg, about nearly everything.
Three-Toed Sloth by Cosma Shalizi, who's a statistician, about statistics and lots of other subjects.
Neal Stephenson isn't literature?
(I think I get what you're trying to convey - I have a separate "Evasion" fiction ebook folder myself - but Stephenson doesn't seem bad or shallow enough to me to deserve getting demoted that way)
I can see everything that's on my desk without moving any of it. This is slightly less true if you count all three table surfaces in my office as "desk," but even if you do that none of the hidden things are books. They're (as I check) button-making apparatus, pencils, and pads of paper.
I don't think I really understand what you're asking for, but here are my current reading habits and a vague idea of the state of my (home) office.
I read mostly textbooks at the moment, but I made time for the library's copy of Siddhartha yesterday. In general I like to keep up with the New Yorker, because it's so well written and edited that everything in it seems to be interesting, regardless of the topic. (I'm currently in the middle of an article about carp.) But that's low priority and I've been busy lately, so for the first time since I acquired the habit I'm a couple of issues behind.
The books on my media list are: 4-Hour Workweek (not planning to read it, but it came up in conversation and I wanted to glance through it), one of PJ Eby's, one of the vipassana books that was recommended by someone here, some fiction recommendations from friends (Beggars in Spain, Kraken), more recommendations from LW (Linguistic Pragmatics, Predictably Irrational, MoR, Refuse to Choose, Home Comforts), some philosophy (the Enchiridion), a couple from my anthropology teacher (Primate's Memoir and an article about tarsiers), and a couple classics I've been meaning to get around to (On the Road and Siddhartha, the latter of which I've now checked off).
I miscounted, by the way. Four table surfaces. One with computers; one with printer, pattern pieces, and flashcards; one with sewing machine and fabric; and one with cutting mat, button-making apparatus and (at the moment) a bunch of sewing-related miscellany, because I dumped out a bag of it while looking for something in a hurry. The only other large groups of my stuff in this room are my fabric stash and mending pile, both of which are pretty sloppy but I don't have a better container handy for either.
As for blogs, check the blogroll at the right of http://inquilinekea.blogspot.com/.
As for books, I've made a huge list at http://simfishthoughts.wordpress.com/books-i-read/ (although it's very unorganized ATM).
Concerning "Guns, Germs, and Steel ": Murray Gell-Mann is involved in some interesting research on general patterns of civilization. But his and Diamond's schemes are just about some general and indirect indicators, not about what the essence of "civilization" is. To get an idea of that, I am curious about instances where "civilization" went down quickly. This puts e.g. "Berlin Diary: The Journal of a Foreign Correspondent 1934-1941", and "Human Smoke: The Beginnings of World War II, the End of Civilization" on my desk. A very remarkable case is told about in Simone Weil's "L'agonie d'une civilisation". I scanned two essay by Zbigniew Herbert on decivilization from this - someone curious to get them? "The Dream of Scipio" by Ian Pears sketches (in typical french history-through-novels manner) a thrilling pattern of several critical moments of the last 1500 years of European history.
Some links: