This page-by-page annotation is organized by sections, as delineated by the seven squares (sprockets) which separate each section. The page numbers for this page-by-page annotation are for the original Viking edition (760 pages). Editions by other publishers vary in pagination the newer Penguin editions are 776 pages; the Bantam edition is 886 pages.
Contributors: Please use a 760-page edition (either the original Viking edition with the orange cover or the Penguin USA edition with the blue cover and rocket diagram there are plenty on Ebay for around $10) or search the Google edition for the correct page number. Readers: To calculate the Bantam edition use this formula: Bantam page # x 1.165. Before p.50 it's about a page earlier; as you get later in the book, add a page.
Finally, profound thanks to Prof. Don Larsson for providing the foundation for this page-by-page annotation.
3.03 The Evacuation
First instance in GR of a lifetime stylistic trait of Pynchon's: unpredictable use of Capitalization. Capitalization is usually applied to nouns, but not uniformly. Often a matter of emphasis. See Mason & Dixon for the widest use, there imitating the writing of the time in which the book is set.
The use throughout all his work might indicate how well-read and influenced by works written before capitalization was standardized Pynchon is.
The full rules of capitalization for English are complicated. The rules have also changed over time, generally to capitalize fewer terms; to the modern reader, an 18th century document seems to use initial capitals excessively. Wikipedia
Besides the normal meanings, including "theater of war", 'theatre' is the name that fireworks' organizers call a sky display.
3.05 iron queen
a queensize bed made of iron. Hardly made after 1900. Queen Victoria had a famous brass (and iron) one in the Crystal Palace! "Beds made of hollow tubes of steel, iron, and brass came to be manufactured in the mid 19th century. These were to be used both by soldiers and civilians. Their main advantage at that time was that unlike wooden beds, these could not be infested with bedbugs. Queen Victoria's brass bed at the Crystal Palace has been the most famous antique brass bed.
By the late 19th century, metal beds were nearly out of fashion." Antique beds []
Also, In The Odyssey, when Odysseus goes to the Underworld, he refers to Persephone as the Iron Queen. Of the four gods of Empedocles' elements it is the name of Persephone alone that is taboo, for the Greeks knew another face of Persephone as well. She was also the terrible Queen of the dead, whose name was not safe to speak aloud, who was named simply "The Maiden". Wikipedia []
3.07 crystal palace
See Alpha entry, especially this re cultural meaning:
The Crystal Palace made a strong impression on visitors coming from all over Europe, including a number of writers. It soon became a symbol of modernity and civilization, hailed by some and decried by others.
In What Is to Be Done?, Russian author and philosopher Nikolai Chernyshevsky pledges to transform the society into a Crystal Palace thanks to a socialist revolution.
Fyodor Dostoevsky implicitly replied to Chernyshevsky in Notes from Underground. The narrator thinks that human nature will prefer destruction and chaos to the harmony symbolized by the Crystal Palace.
When the first major international exhibition of arts and industries was held in London in 1851, the London Crystal Palace epitomized the achievements of the entire world at a time when progress was racing forward at a speed never before known to mankind. The Great Exhibition marked the beginning of a tradition of world's fairs, which would be held in major cities all across the globe. Following the success of the London fair, it was inevitable that other nations would soon try their hand at organizing their own exhibitions. In fact, the next international fair was held only two years later, in 1853, in New York City. This fair would have its own Crystal Palace to symbolize not only the achievements of the world, but also the nationalistic pride of a relatively young nation and all that she stood for. Walt Whitman, the great American poet, wrote in "The Song of the Exposition":
That the Crystal Palace Exhibition "marked the beginning of a tradition of world's fairs" can remind that Against the Day starts at the Columbian Exhibition of 1893 in Chicago. More international optimism.
3.14 second sheep
Compare the narrator’s discussion of William Slothrop’s heretical tract "On Preterition," which argued for the holiness of the preterite, and Weisenburger’s note at 555.29-31.
A wide symbology relates to sheep in ancient art, traditions and culture. Judaism uses many sheep references including the Passover lamb. Christianity uses sheep-related images, such as: Christ as the good shepherd, or as the sacrificed Lamb of God (Agnus Dei); the bishop's Pastoral; the lion lying down with the lamb (a reference to all of creation being at peace, without suffering, predation or otherwise). Greek Easter celebrations traditionally feature a meal of Paschal lamb. Sheep also have considerable importance in Arab culture; Eid ul-Adha is a major annual festival in Islam in which a sheep is sacrificed.
Herding sheep plays an important historico-symbolic part in the Jewish and Christian faiths, since Abraham, Jacob, Moses, and King David all worked as shepherds. wikipedia 
Sheep are often associated with obedience due to the widespread perception that they lack intelligence and their undoubted herd mentality, hence the pejorative connotation of the adjective 'ovine'. In George Orwell's satirical novel Animal Farm, sheep are used to represent the ignorant and uneducated masses of revolutionary Russia. The sheep are unable to be taught the subtleties of revolutionary ideology and can only be taught repetitive slogans such as "Four legs good, two legs bad" which they bleat in unison at rallies. The rock group Pink Floyd wrote a song using sheep as a symbol for ordinary people, that is, everyone who isn't a pig or dog. People who accept overbearing governments have been pejoratively referred to as "sheeple". wikipedia 
adj. (of a mirror) having an incomplete reflective coating, so that half the incident light is reflected and half transmitted: used in optical instruments and two-way mirrors. Collins Dictionary
See the splitting of light all through Against the Day, Pynchon's 2006 novel.
3.19 view finder
as two words, this seems to refer to handheld devices in which slides were slid and viewed in 3-dimensions. Here is a version still being made view finder.
"half-silvered" above seems most correct with this kind of device.
3.22 They pass in line
A Pynchonian leitmotif. The linearity of lining up has resonances throughout his work, articulated most straightforwardly in Against the Day, which starts with "Single up all Lines!", and perhaps dealt with most profoundly in Mason & Dixon, a novel about creating the "Mason & Dixon line".
3.25 Rain comes down
Pynchon's first published story is called The Small Rain. See his remarks on rain in fiction in Slow Learner.
3.30 naptha winters
Naptha is the flammable liquid obtained from the distillation of coal and used to fire gaslights and heaters. ...
3.32 rolling-stock absence
Rolling stock is the collective term that describes all the vehicles which move on a railway.
3.35 Absolute Zero
Theoretical state when no molecules move. Zero. State of entropy, a key concept of Thomas Pynchon's. See early story, Entropy in Slow Learner.
3.36 places whose names he has never heard
'secret cities of poor', deep under these fallen girders. Places that have never been spoken of, yet exist. Lower than Low-lands.
Later in Pynchon's world,in other books, Mason & Dixon and Against the Day, we will travel deeper underground, to places with no names we know, it seems. See a "progressive knotting into", 3.26 in GR.
3.37 the walls break down
See "wall of death" later in Gravity's Rainbow. A-and in Against the Day.
4.01 getting narrower...cornering tighter and tighter
5.03 His name is Capt. Geoffrey ("Pirate") Prentice.
Pirate’s name derives from Gilbert and Sullivan’s operetta The Pirates of Penzance, in which the hero’s nurse has made a fateful error in carrying out her employer’s instructions: Instead of having the boy apprenticed to a (ship’s) pilot, he was apprenticed to a pirate, hence a "pirate ‘prentice." The name, though, is not simply a fortuitous pun: In her error, the nurse has lost a message, like the hare of Herero myth, and thus guaranteed her young charge’s preterition. (There are also connections here to the theme of "communications entropy," which is central to The Crying of Lot 49 and the short story "Entropy.")
5.03 all got scumbled together, eventually, by the knives of the seasons, to an impasto, feet thick, of unbelievable black topsoil
Didn't notice 'scumbled' first time round, I was going too fast. Second read I looked it up. Scumbled? Isn't that some sort of painting [technique? Pynchon make a mistake there? Mean to say scrambled? Hmmmmmmmm. Then I thought of the 'knives' bit, wondered if artists might use a palette knife to do this scumbling business. A Google search for "scumble knife palette " found me this:
"Hard impasto ridges left by the edge of the knife provided the texture I needed to bring the waves crashing in."
Impasto eh? I thought that just meant paste. So the knives in "knives of the seasons" makes perfect sense. And Dictionary.com throws up another interesting nugget:
A-and the wonderful phrase, "knives of the seasons" embodies another lifelong deep theme in Pynchon's work: that the 'wheeling' of time [see later in Gravity's Rainbow and Against the Day], the cycle of nature, is an ineluctable good thing, even as it knifes us, ravages, us. It thickens us, impasto-like, gives us topsoil in our characters, so to speak.
"To blur the outlines of: a writer who scumbled the line that divides history and fiction."
Suggests the double-helix structure of the DNA molecule that preserves the "living genetic chains" evoked at 10.14.
Cf. p. 209, Mason & Dixon: " oblique angles with all meridians and that is a spiral coiling round the poles but never reaching them."...
7.09 Pick bananas
Pirate's decision after a paragraph on the inevitablity of the rocket's flight can remind one of a famous Buddhist sutra on picking a strawberry: The Sweetest Strawberry
Buddha told a parable in a sutra:
A man traveling across a field encountered a tiger. He fled, the tiger after him. Coming to a precipice, he caught hold of the root of a wild vine and swung himself down over the edge. The tiger sniffed at him from above. Trembling, the man looked down to where, far below, another tiger was waiting to eat him. Only the vine sustained him. Two mice, one white and one black, little by little started to gnaw away the vine. The man saw a luscious strawberry near him. Grasping the vine with one hand, he plucked the strawberry with the other. How sweet it tasted!
-Paul Reps, Zen Flesh, Zen Bones
from Everyday Mind, edited by Jean Smith []
Beyond the Zero
Un Perm' au Casino Herman Goering
In the Zone
279-295, 295-314, 314-329, 329-336, 336-359, 359-371, 371-383, 383-390, 390-392, 392-397, 397-433, 433-447, 448-456, 457-468, 468-472, 473-482, 482-488, 488-491, 492-505, 505-518, 518-525, 525-532, 532-536, 537-548, 549-557, 557-563, 563-566, 567-577, 577-580, 580-591, 591-610, 610-616