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.
An autoclave sterilizes equipment and supplies by subjecting them to high pressure saturated steam at 121 °C for around 15–20 minutes depending on the size of the load and the contents. It was invented by Charles Chamberland in 1879, although a precursor known as the steam digester was created by Denis Papin in 1679. The name comes from Greek auto-, ultimately meaning self, and Latin clavis meaning key — a self-locking device. 
The "fine clutter of steel bones" inside the autoclave should sensitize us to other hot enclosures to come -- domestic, folkloric, and genocidal. This is reinforced at once by patients' cries of pain "as from cold metal."
47.34-35 run three times around the building without thinking of a fox and you can cure anything
Pynchon's source may be folkloric, shared with Douglas Hofstadter -- who in Godel, Escher, Bach (1979) would illustrate paradox by citing "this surefire cure for hiccups: 'Run around the house three times without thinking of the word "wolf."'"
Note that an injunction not to think of something is a perfect example of anthropologist Gregory Bateson's "double bind." Pointsman's own thinking may have absorbed a bit too much of the "paradoxical state" and "idea of the opposite" he studies.
48.13-14 sybilline cries arriving out of the darkness
Copy editor napping: "Sybil" is a woman's given name. Sibyls were female oracles in classical times. The Sibyl, with frenzied mouth uttering things not to be laughed at, unadorned and unperfumed, yet reaches to a thousand years with her voice by aid of the god. - Homer 
Abreactions of the Lord of the Night
Abreaction is a psychoanalytical term for reliving an experience in order to purge it of its emotional excesses; a type of catharsis. Sometimes it is a method of becoming conscious of repressed traumatic events. 
48.25 " . . . one of Lazslo Jamf’s subjects . . . "
The name "Jamf" apparently derives from an acronym used by Charlie Parker: "Jive-Ass Mother-Fucker"!
48.38 Transmarginal and Paradoxical phases
49.26-29 pain-voices of the... Lord of the Night's children... sooner or later an abreaction
The quick repetition of these ideas within two pages, here, seems to dig at the idea that Pynchon is inferring that the aural psychical effects of the bombing victims come after the fact of death just as the bombs sound come after their delivery. In other words, because of the instantaneous nature of their death there is much psychic energy that is let off which affects the environment afterward, ie. all over the frost & harrowed city.
49.30 ...as once again the floor is a giant lift.. the walls blown outward This paragraph takes us into the drugged, traumatized dreams and memories of the "rocketbombed" patients, narrated in second person: "your sudden paralysis...the sight of your blood spurting..."
We might later recall that voice and several of the fragmentary images --"The cinema kiss never completed... crying from the rows either side... the sudden light" -- if we find ourselves in another movie theater, if we remember, if there is time.
Strictly speaking, a mummer is an actor in a traditional seasonal folk play. The term is also humorously (or derogatorily) applied to any actor. 
A palimpsest is a manuscript, usually parchment or vellum, from which the text has been scraped off and which can be used again. Over time the earlier writing can re-emerge, creating multiple superimposed layers -- symbolic of the mind as well as history. 
Realpolitik refers to politics or diplomacy based primarily on power and on practical and material factors and considerations, rather than ideological notions or moralistic or ethical premises... Realpolitik is a theory of politics that focuses on considerations of power, not ideals, morals, or principles. 
51.04 you are the Traveler's Aid
The Travelers Aid organization began with an 1851 bequest from St. Louis mayor Bryan Mullanphy. Its efforts were directed first to settlers traveling West, and later became worldwide (including a role in the USO -- United Service Organizations -- supporting Allied troops in WWII.)
One of Travelers Aid's early concerns was to protect stranded female travelers from the over-hyped "white slave trade." That gives ironic poignance to Pointsman's tenderness -- "for the moment," that is.
51.06 AWOL bag AWOL = "away without [official] leave." An AWOL bag is a small unframed man's bag with handles, usually leather or canvas. It was named for its convenience as "grab and go" luggage into which a weekend's clothes could be hastily tossed.
The name is Pynchon’s but evokes "The Cobb," the famous jetty at the city of Lyme Regis on the southern coast of England.
Regis is the Latin genitive of Rex, "the King" thus, "of the king."
As William Safire notes, "The colloquial noun and interjection ick, as well as its adjectival form, icky, are terms of disgust, distaste and revulsion." Oedipa Maas uses the term in CoL49 in response to a grisly play.
Combining Ick and Regis, could therefore render the anarchic sentiment "sick of the king."
Ick Regis, when spoken aloud, sounds like 'egregious'--perhaps a comment on the programs being run at the White Visitation?
Interestingly, for PISCES and White Visitation to be headquartered in a place named Ick Regis, brings associations with the fish sickness "ick" also known as the white spot disease, which is a severe dermatitis of freshwater fish caused by a protozoan of the genus Ichthyophthirius and is especially destructive in aquariums and hatcheries called also ichthyophthiriasis, ichthyophthirius. Hence, the "white visitation" could, again, be a sickness.
52.23 it's the damned Rundstedt offensive
Pointsman ascribes his tight budget to high-level concerns over the German counteroffensive in Belgium, France, and Luxembourg (not Holland, per Weisenburger) that would be remembered as the Battle of the Bulge. Freedictionary and Wiki. --Jpicco
Deptford is a district of south London, England, located on the south bank of the River Thames. It is named after a ford of the River Ravensbourne, and from the mid 16th century to the late 19th was home to Deptford Dockyard, the first of the Royal Dockyards... Deptford experienced economic decline in the 20th century with the closing of the docks, and the damage caused by the bombing during the Second World War: one V-2 rocket alone destroyed a Woolworth's store outside Deptford Town Hall, killing 160 people. 
53.03 "'One, little, Fox!'"
Compare with Spectro's use of "fox" for patients (47.34), now recast as Pointsman's prey -- the ultimate lab animal. "Fox" recurs nearly twenty times in the novel, often with eerie connotations (e.g. 138.23).
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