I started my second Twin Peaks rewatch last night with the pilot (I rewatched FWWM last week already). I'm going to try to watch an episode a day in the vein of the timespan of each episode. Anyways, anything I jot down may be very obvious to most or something you hadn't caught before, but I'm not counting on the latter. And it includes things I'll keep written down to remember later on and connections with FWWM.

Pilot

-Catherine ignores Peter when he says he's going fishing. This foreshadows their long battle of insubordination through the series, more on Catherine's part, of course.

-Lucy tells Truman to answer the black phone. This symbolizes the very dark news he is about to receive. 

-The plastic Laura is wrapped comes off more as white than transparent. White symbolizes innocence. Innocent is what she came off as on the outside.

-Sarah is a heavy smoker, something we can see in FWWM as well.

-Ben's reaction to Laura's death makes me wonder if they had the whole One Eyed Jack's thing planned from the beginning. 

-There was a brief focus on the twin around Ronette's hands. 

-Shelly is watching a news piece on Ronette when Leo confronts her about the cigarettes.

-Teresa Banks: no family, no one claimed her body. Connection with FWWM.

-"Leland made it through the day somehow". Never fails to make me wonder. 

-The pilot marks the first instance of a Cooper thumbs-up.

That's all for now, folks. Stay tuned!

I just finished episode 1.01, and enjoyed it a lot. It feels great to rewatch the show while writing down anything significant and knowing everything that's gonna happen later on. Here are the annotations for tonight, forgive anything obvious or insignificant:

1.01

-As per his matutine recording to Diane, Cooper once stayed in a hotel in El Paso.

-According to Audrey, emotional problems run in the Horne family. 

-Audrey asks Cooper if he ever gets itchy palms. Foreshadowing TLMFAP rubbing his palms together?

-The Doc tells Harry and Cooper about the bite marks on Laura. We later find out Waldo the bird is responsible for this.

-He also says Laura had sex with three men that night. Jacques, Leo and Leland (?).

-FWWM Connection: Leo's bloody shirt. I don't recall Jacques or Leo using it to wipe blood, though. Retconning, anyone?

-The picnic video was shot two weeks ago.

-James said that something had scared Laura. This is answered in FWWM, which is Leland having sex with her while she slept.

-It always struck me as weird that Laura in the necklace flashback and Laura in FWWM are so different, the former seeming much more joyful. A rich contrast!

-First mention of Jacques when Ed tells Harry that his drink was spiked. Also, first instance of Bookhouse Boys signal between Ed and Hawk.

-Cooper is compiling his list of J's, evident when he asks if "Johnson" is spelled with a "J".

-FWWM Connection and season 2 plot: Meals on Wheels.

-The Log Lady saw Laura the night of her death. 

-James was 10 when his father died.

Naturally, I got more notes this time because of the shift in style near the end. Most of the notes involving Leland and Cooper's dream are a blend of personal theories and stuff I've read online.

1.02

-OEJ girls are recruited at the perfume counter.

-First appearance of Blackie, who is featured prominently during the first few subplots of season 2.

-Audrey helps Cooper with his investigation by telling him about OEJ.

-Who is the man with Leo? It looks like Leland, but I can't think of any reason why he'd be there.

-I never understood Leo's comment about the old lady giving it out until now: he knows Shelly is cheating on him. He's cheating on her, as well, so to hell with him.

-Nadine's super strength subplot foreshadowed when she bends the exercise machine?

-Audrey says Ben used to sing to Laura.  This is probably how she knows Laura used to work at OEJ.

-Bloody cloth found near crime site. Don't recall the story behind this much from my previous rewatch.

-2nd Cooper thumbs-up.

-Leland is playing cheerful music, and he's dancing a bit, too. Is this a manifestation of Bob's sorrow over not being able to possess Laura? 

-Cooper can dream the future, as seen in FWWM. He's dreaming himself 25 years later, but why isn't Laura aged? Or is she? She sure looks different from what she looks like in the necklace flashback and FWWM. Mike is telling Cooper the whole story to punish Bob, who has been hoarding the garmonbozia. 

-FWWM Connection: Let's Rock.

-Laura touching nose: referencing her cocaine use.

-That gum you like: a way to remind Cooper of this later on when Leland/Bob says that the gum used to be his favorite as a child, possibly before he was possessed. 

-She's my cousin: reference to Maddy.

-She's filled with secrets: reference to Laura's second life as a prostitute and drug addict. 

-The birds: reference to Waldo and possibly the owls.

-Always music in the air: reference to the ongoing record at the cabin, also to indicate that Cooper is on the right tracks.

-I feel like I know her: Maddy possibly hadn't reunited with Laura in a while, so she knows her just a bit.

-My arms bend back: reference to the twine.

1.03

-Audrey appears to want to start her own investigation. I assumed she was pointing Cooper to OEJ's because Laura worked there, but now she claims she doesn't know if she did work there.  This is very ambiguous.

-Break the code, solve the crime: the M.O. of a true Twin Peaks fan. MODUS OPERANDI.

-Coopers says that Mike shot Bob when he was reformed. Could he have shot Robertson or another previous vessel of Bob's, making him move on to Leland's body?

-This episode marks the first appearance of Maddy

-Albert says that they found a small plastic artifact with the letter J on it. Was this ever explained?

-Nadine tells Ed that she used to watch Norma during high school games. 

-I always considered Shelly a bitch because of the way she mocks the casket incident at the diner. The incident itself, however, was unintentionally amusing.

-Jacques starts to materialize: the Bookhouse Boys know he distributes drugs to high school students.

-The Bookhouse Boys have been around for 20 years.

-Bernard Renault is a janitor at the Roadhouse, something I didn't catch before.

-Josie tells Harry that Ben and Catherine are going to hurt her. Is she doing this so that he can protect her, or was she planning on approaching Ben with a deal?

"Harry, I'm going to let you in on a little secret. Every day, once a day, give yourself a present. Don't plan it, don't wait for it, just let it happen. Could be a new shirt at the men's store, a catnap in your office chair, or two cups of good, hot, black coffee. Like this."  -Dale Cooper

 Yes. Later in the series, Albert show's Cooper a reconstruction of the plastic piece that his team made, which shows it to be part of a One Eyed Jacks poker chip. This also fits in with Jacque's "bite the bullet baby" monologue at OEJ.

nice one to read with morning coffee.

keep it up!

1.04

-Leland is mocking Sarah's vision claims. Or is this Bob?

-Laura was seeing Jacoby for six months.

-Cooper's story about a broken heart foreshadows the arc with Caroline and Windum. It's amazing how everything was planned and established in this show!

-Ben meets Leo to pay for arson. This was something unclear to me the first two times around.

-Laura knew about Sarah and her visions, according to Donna.

-Hank is supplying Ben with Leo's services.

-Hank is associated with Josie.

1.05

-Blood on Leo's shirt is AB negative, Jacques' blood type. If I remember correctly, there's a gaffe later on about this?

-James' mom is a prostitute, as was Laura. Must be hitting him hard.

-Why would Jacques buy 50 gallons of oil? So that Leo can burn down the sawmill.

-Maddy says that she feels like she knew Laura, which was foreshadowed in Cooper's dream.

-FWWM Connection: Bobby rhetorically asks Jacoby if he's ever killed somebody.

-FWWM Connection: Laura used Bobby for drugs.

-"Into the Night" is always playing in the cabin. Connected to Cooper's dream. Also, I wish I had known more about Julee back then, because the scene is much more powerful now.

-Ben is working behind the scenes with Josie. 

Reading your annotations and observations makes me wanna see TP for the 4th time.

Brilliant!

Thank you........

Thanks for the compliment! It's very fun to take notes while rewatching this show. Unfortunately, the note value has lowered since the pilot.

1.06

-Cooper doesn't like birds.

-Emory's notebook lists dates for 1990, when the show is supposed to be set in 1989. Could this be when the girls who work there turn 18? It would fit with the age of consent for the brothel, and it's the only thing I can think of.

-FWWM Connection: Waldo saying lines from the cabin scene.

1.07

-The episode opens with a canvas of palm trees and a beach setting. I find this a genius contrast to the usual opening involving the mountains and the Douglas firs of Twin Peaks.

-So Bob attacked Jacoby because his next target is Maddy, right?

-The whole Sawmill conspiracy seems to be well-written and consistent so far. We have Hank going to jail in order to not be implicated in Andrew's death, Leo being shot by Hank to get rid of witnesses and Josie goes off to shoot Cooper before leaving for Seattle. 

Yes, this is all that was worth writing in the last two episodes of the season. Season 2 will probably provide much more annotations due to the way it starts, what with the return of the mythos.

 I think Leo used gasoline to burn the mill.  The heating oil really was for the cabin.

 This is fun to read.

I just finished 2.02. It was an amazing viewing and I'm glad to have compiled two and a half pages of notes, just like when I first started this rewatch. I hope future episodes give me this much to write down!

2.01

-Does the waiter struggle hanging up the phone because Lodge spirits don't use them much?

-Cooper is left-handed.

-Third Cooper thumbs-up.

-Is the Giant benign?

-Ring symbolizes full-circle, which is when Cooper should be getting it back.

-Cooper says it's not bad getting shot as long as you can keep the fear out of your mind. This is what kept Laura going all those years.

-Leland's first real kill is making Bob's presence more visible.

-Maddy is having visions too. Does this run in the family?*

-Fourth Cooper thumbs-up to Andy.

-Laura allowed herself to be killed, Jacoby's theory and the true thing.

-This episode marks the first mention of the oil stench whenever Bob is around.

-Jonathan's first appearance, and Josie's backstory starts to materialize.

2.02

 -Albert says the waiter doesn't remember anything from the night Cooper was shot. Later on, we learn Leland never remembered anything whenever Bob took over. The Giant was possessing the waiter the whole time during that scene.

-First mention of Windum Earle, another great example of establishing things early on.

-Pierre, and probably the other Lodge spirits, can manipulate garmonbozia or any form of creamed corn.

-The grandmother and grandson go to where they need to be, using the name of the person they're impersonating.

-Ronette recognized Bob from her nightmare the night before.

-The Log tells Briggs to deliver the message, which we find out later on to be the message picked up from deep space.

-Hank and Truman grew up together and he used to be a Bookhouse Boy.

-Leland remembers when he was possessed as a boy. Does Bob take over later on by lying about the location? I will build a better interpretation once that storyline ends.

-Who the hell tries to contact Truman? Did we ever find out?

-Laura was thrown out of One Eyed Jack's for doing drugs. Ironically, much worse things go on there.

-The owls are not what they seem: possibly the Lodge telling Cooper that he hasn't diverged from the trajectory placed by the Giant? The spirits travel through owls, I presume.

 *Theory I thought up at the end of the episode: future victims of Bob see him in visions so that they're traumatized by the time he goes to attack them. Sarah started seeing him before Maddy, but she was never attacked in the show. She was, however, drugged by Bob.  

"Harry, I'm going to let you in on a little secret. Every day, once a day, give yourself a present. Don't plan it, don't wait for it, just let it happen. Could be a new shirt at the men's store, a catnap in your office chair, or two cups of good, hot, black coffee. Like this."  -Dale Cooper

in philip jefferies's breakdown, we see the tremonds/chalfonts in the room, on the couch, maybe above a convienence sort like MIKE says in the ep.2 cooper dream.
BUT
Thats FWWM, not TP. do all the rules have to be the same between series and film? im not so sure about that.

How does that contradict the show? I if anything, it supports the theory more as FWWM confirms that they are Lodge spirits.

Also, I told another TP fan about my dissecting project and he said taking notes while watching a film or TV series is freaky. I pity such close-mindedness. But then again, his life ambition is to become a PE teacher.

2.03

-"B" found under Ronette's fingernail. Leland/Bob must have gone there the night before after finding out she was being kept there.

-Hilarious Albert line about Leo appearing as Mr. Potato Head at the hospital.

-No agency can find Bob because he doesn't exist in the real world.

-This episode marks the first, and sadly not last, appearance of Dick Tremain.

-Leland can flick matches because Bob is an expert at it.

-Lucy announcing her pregnancy to Dick was louder and even mean, foreshadowing that she's gonnastay with Andy in the end.

-James foreshadows his terrible motorcycle escapades with a line about getting on his bike and leaving. Also, him knocking all that stuff off the table and following Donna outside is hilarious.

-First appearance of the last Renault brother, Jean.

-Without chemicals, he points: Mike can see Bob. He probably reacted to the wanted poster this time and not last because he was closer to needing the medicine this time around.

2.04

-Jean Renault sells insurance to OEJ's. 

-Harry tells Cooper he'll have a Bookhouse Boy at the Roadhouse at 9:30, a reference to important meet-ups happening there at that time.

-Donna tells Maddy she'll survive the love triangle. Is this foreshadowing Maddy's death?

-A nice The Elephant Man reference I always noticed: Judge Sternwood asks Leland if the facilities have been adequate, and Leland answers that everybody's been so kind, not unlike when Car Gomm asks John Merrick the same thing and gets the same answer.