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.
42.07 whose name will be Vladimir (or Ilya, Sergei, Nikolai...)
These recall the Russian names assigned to laboratory dogs in Pavlov's experiments. This wild or abandoned dog, "never having been near a laboratory in his life," will be given such a name: the first assertion of the control that Pointsman craves above all.
42.35 Balaclava helmet
...a form of headgear covering the whole head, exposing only the face or upper part of it, and sometimes only the eyes and mouth. More typically known today, in various forms, as a ski mask.
The name "balaclava" comes from the town of Balaklava, near Sevastopol in Crimea (now Ukraine). During the Crimean War, knitted balaclavas were sent over to the British troops to help protect them from the bitter cold weather. They are traditionally knitted from wool, and can be rolled up into a hat to cover just the crown of the head. http://en.wikipedia.org/wiki/Balaclava_(clothing) Jpicco 09:53, 16 May 2009 (PDT)
43.28 instead I'm with this gillie or something
Ghillie or gillie is a Scots term that refers to a man or a boy who acts as an attendant on a fishing, fly fishing, hunting, or deer stalking expedition, primarily in the Highlands or on a river such as the River Spey. Jessica is mocking Roger's role tonight as Pointsman's assistant. A ghillie may also serve as a gamekeeper employed by a landowner to prevent poaching on his lands, control unwelcome natural predators such as fox or otter, and monitor the health of the wildlife. 
44.09 "this isn't Kenya or something"
I.e., not big-game hunting (Kenya was then a British colony) with Roger as beater, driving animals into the open for Pointsman to shoot. See also "'Moment-- of truth!'" on line 38 below, borrowed from the matador's kill in bullfighting. The two manly, exotic comparisons frame another, with a famous pet collie -- and all three are comically inappropriate with this chase after a potential lab animal.
44.17-18 "Why it's Mrs. Nussbaum!"...Fred Allen..."You vere ekshpecting maybe Lessie?"
Pansy Nussbaum was a Jewish housewife character on Fred Allen's radio show. 
See more about the actress, Minerva Pious, who played Mrs Nussbaum here. On the Fred Allen Show, she often said the lines "You were expecting maybe..." in a thick Yiddish accent.
This section of the novel is so cartoonish, I can't help thinking of Merrie Melodies in general and a specific Bugs Bunny episode called French Rarebit in which a French cook with a thick accent says "You were expecting maybe Humphrey Bogart." The video is up on dailymotion.
44.22 "Pointsman just wants to count the old drops of saliva..."
This was the setup for Pavlov's classic early experiments: dogs were conditioned to associate feeding (and their natural salivation) with a bell. Once the new response was established, they would salivate at the sound of the bell alone. A surgically implanted drain from the salivary ducts allowed measurement of the strength of the response.
45.16 "Do you have any cigarettes?" asks Jessica.
Her nonchalance amid collapsing prams, flailing nets and "a system of lever arms that can plunge them into deadly collapse at any moment" tells us that she knows slapstick when she sees it. Pynchon alternately encourages and undermines our readiness to cast Jessica as the more tender/emotional of the couple.
45.40 “We’re for it”
Or "in for it," in US idiom.
46.32 not toward any apical God God at the apex: the top of a cathedral spire or church steeple. (Or of the Chain of Being, p. 77.)
46.41 St. Veronica
Saint Veronica, according to the "Acta Sanctorum" published by the Bollandists (under February 4), was a pious woman of Jerusalem who, moved with pity as Jesus carried his cross to Golgotha, gave him her veil that he might wipe his forehead. Jesus accepted the offering and after using it handed it back to her, the image of his face miraculously impressed upon it... The closest reference in the canonical scriptures is the miracle of the woman who was healed by touching the hem of Jesus’ garment (Luke 8:43–48); her name is later identified as Veronica by the apocryphal "Acts of Pilate". The story was later elaborated in the 11th century by adding that Christ gave her a portrait of himself on a cloth, with which she later cured the Emperor Tiberius. 
47.03 The Book
Weisenburger identifies this as volume 2 of Pavlov's Lectures on Conditioned Reflexes, "his effort to branch out of physiological studies and into psychology." It was published in Russian in 1940, translated into English 1941.
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