- Please keep these annotations SPOILER-FREE by not revealing information from later pages in the novel.
Page numbers refer to editions with 369 pages, where the story begins on page 1. Not sure if there are other editions with variant pagination. Please let us know otherwise.
Doc called Sancho next morning
Morning, Saturday, March 28, 1970, the fifth day of the narrative.
Ginger . . . Skipper . . . Gilligan . . . Thurston Howell III . . . Lovey
All are characters from the 1960s TV show Gilligan's Island. The "code" would presumably be whether the aspiring actress (Ginger/Shasta) would end up with Gilligan/Doc, or whether she would end up with the rich man (Thurston Howell III/Mickey Wolfmann), who might or might not ever divorce his wife (Lovey/Sloane Wolfmann).
Varathane is a brand of wood stains and polyurethane sealants.
The largest city and capital of the US Virgina Islands.
Like new debt... from institutions in places like South Dakota that you send away for by filling out the back of match cover
Sauncho's quote here echoes almost exactly Zoyd's thoughts in Vineland in regard to Isaiah Two Four's business proposition: "expecting some address in a distant state, obtained from a matchbook cover." (p. 19, Vineland)
An error. Should be "Joseph Arnould", who wrote Law of Marine Insurance (1848).
There were two men (father and son) named Theopilus Parsons in the nineteenth century. This reference is to the younger one, who published A Treatise on the Law of Marine Insurance and General Average in 1868.
Your stomach isn't it.
A listless way of saying "It's your stomach, so feel free to order whatever horrible food you desire."
Another reference to Gilligan's Island. "L'il buddy" was the captain's nickname for Gilligan. See page 89 for another instance of Doc being linked to Gilligan.
Also, Hector calls Zoyd this in Vineland, see p. 26. The contraction is spelled li'l in Vineland but l'il in Inherent Vice. The former is technically correct, since the elision (the "tt") is after the "i" rather than before it.
A perhaps obvious pun on Il Trovatore, the Verdi opera.
a tremendous nitroglycerin explosion in Halifax Harbor
The largest accidental explosion in history. 
This name is likely derived from a 1910 noir-ish murder-mystery novel Paternoster Ruby by Charles Edmonds Walk. Alexander Stilwell Burke and Stodger, a plain-clothes cop, are two main characters. Google Books Perhaps Pynchon's slyly recycling here some unused stuff from his vast research for Against the Day? A excerpt from Walk's novel:
- "Nasty case," Stodger was imparting, in queer staccato sentences. "Shouldn't have much difficulty, though; responsibility lies between two men. Here all last night. Nobody else. Callahan and O'Brien holdin' 'em. One 's Page's private secretary; fellow named Burke Alexander Stilwell Burke. Peach of a monicker, ain't it? Has all three sections on his cards.
- Suddenly she snuggled closer and clasped her hands tightly upon my shoulder. Her hair teased my cheek, and the delicate perfume of it made me light-headed. Twisting her pretty head sideways, she flashed an arch look at me from under her lashes, then glanced quickly away again. Blue eyes and long dark lashes are a potently disturbing combination.
- "Well," she sighed, "the Page case may have cost you a fortune, but it gave you me. And I for one am very content and happy, Mr. Swift."
a three-hour tour
Yet another reference to Gilligan's Island. This is a quote from the theme song.
Hoover Library at Stanford
The Herbert Hoover Presidential Library--not J. Edgar.
Well, it could be a reference to throwing folks into the deep blue sea. However, in the 1970s, long before Guantanamo Bay, Abu Ghraib and "enhanced interrogation," Britain utilized “deep interrogation” techniques in an effort to defeat the Irish Republican Army. Constitutions in Crisis: Political Violence and the Rule of Law by John E. Finn (Oxford University Press, 1990) examines how the efforts of two western liberal democracies, the United Kingdom and the Federal Republic of Germany, to cope with domestic terrorism threatens their constitutional integrity. Finn argues first that widespread political violence challenges the presuppositions of constitutional authority in any liberal democracy, namely that reason and deliberation, and not passion or will, can be the basis of political community. He defines "deep interrogation":
- "Deep interrogation" a bureaucratic phrase which takes the place of the simpler word "torture" and is worth of Orwell's 1984 is on a different level of immorality than hysterical sadism or the indiscriminate bomb of urban guerrillas. It is something organised with imagination and a knowledge of psychology, calculated and cold blooded ...  (Buy it...)
Pronounced zoo'-keys, Zucky's was run by Zucky and Hy Altman, founders of the SOVA food pantries, and frequented by such celebrities as Governor Arnold Schwarzenegger - who would meet there for breakfast every morning before continuing on to the gym, back in the day. Closed since 1993, it was located at the corner of Wilshire and 5th Street, in Santa Monica. It was one of the few places open after 10pm in Santa Monica.
Marcus Welby, M.D.
Hour long medical drama that aired on ABC from '69-'76. Took place in Santa Monica and ranked first in Nielsens for the year 1970. View the opening credits where Zucky's sign appears on the left side at :08 in.
what Cheech and Chong might call matzo-ball jones?
Punned reference to "Basketball Jones", song on Cheech and Chong "Los Cochinos" album with release date 1973.
Raymond Chandler's famous detective, featured in Chandler's many novels set in LA, including The Big Sleep (1939; his first appearance), Farewell My Lovely, and The Long Goodbye.  There are many important parallels between Pynchon's Doc and Chandler's Marlowe, especially his world-weariness, his fondness for certain drugs of choice, and a penchant for cracking wise and getting beaten up and worse. (John D. MacDonald's fictional detective Travis McGee is also an important predecessor; see below). Of all Chandler's fiction, Farewell My Lovely (1940), which many think is Chandler's best, may be most relevant for the plot and themes of Inherent Vice. For instance, in that novel Marlowe stays in a hotel in Venice Beach before going out to Laird Brunette's offshore gambling boat, the Montecino. Farewell My Lovely also has "rehab" centers that serve as a front for torture and murder; characters with hidden identities; an impossibly convoluted plot; and a literary style that features striking metaphors, similes, and literary allusions. Marlowe is, like Doc, a dark mixture of cynicism, doggedness, and indifference--yet his goodness and inherent virtues can't be killed. To trace the parallels with Chandler's Marlowe, though, is to see how fully Pynchon has transformed and deepened the generic conventions of 1930s and '40s detective fiction (and film noir inspired by it) even as he pays homage to these.
Dashiell Hammett's detective in The Maltese Falcon (1930) and other crime fiction; in John Huston's famous film based on the novel, he's played by Humphrey Bogart. 
Johnny Staccato is a private detective series which ran for twenty-seven episodes on NBC from 1959-1960. Title character Johnny Staccato, played by John Cassavetes (1929-1989), is a jazz pianist/private detective. 
Krazy Kat was a popular comic strip that ran in newspapers from 1913 to 1944. Ignatz and Offisa Pupp are characters.
"but nowadays it's all you see anymore is...fuckin cop shows"
Compare with today's television being saturated with programs which typically feature forensics specialists who inexplicably have the authority to make arrests and conduct interrogations, and are still "just being regular guys, only tryin to do their job, folks, no more threat to nobody's freedom than some dad in a sitcom."
"Why not get a houseboat up in the Sacramento Delta--smoke, drink, fish, fuck..."
It's tough not to see this as a nod to Doc's brother shamus Travis McGee, the creation of Florida writer John D. MacDonald. McGee lives on a houseboat, taking his "retirement in installments," drinking, lounging on Florida beaches, meeting and inevitably helping beautiful women out of troubles that almost always involve a sinister land broker or two. Along the way Trav usually ends up pontificating about rapacious land developers, the increasingly artificial and isolated American lifestyle, and people's loss of connection with the natural world. 
Sunrise was on the way
Early morning, Sunday, March 29, 1970, the sixth day of the narrative, and Easter Sunday.
- March 29 doesn't quite jibe with "It was late winter in Gordita" (line 5) or, on page 102, "the wintertime smell of crude oil..." (line 11). Spring comes sometime between the 19th to the 23rd of March, so according to Pynchon here we're sometime before March 29, yes?
Here is the weather for March 29--a pretty average day by L.A. standards.
[T]he engine sounds were not passing across the sky where they should have . . .
An apparent allusion to the opening line of Gravity's Rainbow. As a consequence of this, "everybody's dreams got disarranged," which also seems to be happening on GR's first page.
two plastic skegs
A skeg is a fin attached to rear of a surfboard.
Big wave in Northern California. Trivia alert: apparently named after a dog who swam out with the first people who tried, but failed, to surf the wave. While no one was surfing this now famous wave until the mid-70s, it had been known about at least since 1961. Video.
This is a surfing/skateboarding term for someone who rides left-footed. So-called regular foot riders keep their left foot at the front of the board, but goofyfoot riders put their right foot at the front. More here.
Doc, also up early
Early morning, Sunday, March 29, 1970, the sixth day of the narrative.
a surfer or two who'd found and ridden other breaks [...] unphotographed and unrecorded
Even though Pynchon's reference to Mavericks would seem an anachronism, as no one other than a couple surfers had even tried Mavericks until Jeff Clark began riding the gigantic break in 1975, alone, until 1990 when he convinced some other surfers to check it out, this description would seem to fit Jeff Clark perfectly, discovering and surfing, alone, some of the largest waves on the planet. Jeff Clark Wikipedia entry... Pynchon himself, as we all know, likes to remain unphotographed.
Surfaris laugh . . . "Hooo-oo-oo-oo---Wipeout!"
The original Dot label version of "Wipe Out" has the laughter on it that Zigzag and Flaco are arguing about, not the later, and less well-known, Decca re-recording. The Surfaris and "Wipe Out" have a surprisingly tangled history:
- Dot records was the national distributer of "Wipe Out" and the label quickly wanted to capitalize on its success, but rather than use the Surfaris they had The Challengers do covers of other intrumental hits. The only songs that are from the Surfaris on the "Wipe Out" LP are the 2 sides of that single. After the single took off they were quickly brought in to tape an album. It was in the can 12 hours later. Only a week went by before it was out in the record bins. This was a big surprise to the Surfaris. They were even more surprised realize that aside from "Wipe Out" and "Surfer Joe" the remainder of the LP was not them! When they confronted their manager (The Laugh guy in the "Wipe Out" intro), he told them the producers had to add a few overdubs and to listen closer. The more they listened the more they doubted this story. Finally the manager admitted that union musicians had been brought in to do the songs they had recorded. When they realized they had no legal binding contract from Dot records they went off in a huff to Decca records and recorded their real debut LP, "The Surfaris Play". They were required to re-record "Wipe Out" as Dot did have the rights to it! 
"Barney" in this context refers to the character Barney Fife from The Andy Griffith Show an American sitcom which aired on CBS from 1960-1968. Fife was an incompetent blowhard who was overly zealous as a police officer and was played by Don Knotts (1924-2006) More on the Barney Fife character...
in the slow seep of dawn
Early morning, Sunday, March 29, 1970, the sixth day of the narrative.
A Zen Buddhist discipline which recommends "just sitting".
A high school in Manhattan Beach, CA.
Soil layer rich in iron oxide, formed in tropical and sub-tropical regions. Wikipedia
"Earth has an immune system, too...like the oil industry"
Recalls Kurt Vonnegut's quote, "We're terrible animals. I think that the Earth's immune system is trying to get rid of us, as well it should." From his appearance on The Daily Show with Jon Stewart.
Atlantis and Lemuria
The mythical continent of Lemuria is mentioned throughout Inherent Vice. Shasta Fay Hepworth's namesake, Mt. Shasta in Northern California is believed by some to be the home of Lemuria's survivors.
Owsley Stanley. Famous large-scale supplier of LSD.
Doc's name then was something like Xqq
Doc's name, and the dual-sun planet on which he resided, is reminiscent of Italo Calvino's Cosmicomics (1965) which takes place billions of years ago before Earth and on an early Earth, and has characters with names such as Qfwfq and (k)yK and Lll. Each story takes a scientific "fact" (though sometimes a falsehood by today's understanding), and builds an imaginative story around it. From the dustjacket blurb:
- The narrator, Qfwfq, spends his childhood in the soundless, timeless void; among the incandescent colors of stellar explosions, he plays with hydrogen atoms like marbles and, sitting astride a galaxy, chases his friend Pfwfp around the firmament. Or, as an adolescent on the new Earth, he has his first shy love affairs with Ayl, Lll, and Mrs. Vhd Vhd...
A chemical element that has the symbol Os and atomic number 76. Osmium is a hard, brittle, blue-gray or blue-black transition metal in the platinum family, and is the densest natural element.
you'll be the same size and density
This discussion of Doc's "density" is reminiscent of Mondaugen's Law in Gravity's Rainbow: "Personal density [...] is directly proportional to temporal bandwidth":
- "Temporal bandwidth" is the width of your present, your now. It is the familiar "delta t" considered as a dependent variable. The more you dwell in the past and in the future, the thicker your bandwidth, the more solid your persona. But the narrower your sense of Now, the more tenuous you are. It may get to where you're having trouble remembering what you were doing five minutes ago, or even as Slothrop now what you're doing here, at the base of this colossal curved embankment... 
Well, Doc, transported to Earth 3 billion years in the future, is certainly dwelling the future and indeed his density is very high. However, the Doc we've come to know here more closely seems to fit the description of someone with a very narrow "sense of Now."
They were outside on the beach, it was nighttime
Night, Sunday, March 29, 1970, the sixth day of the narrative.