Event Flags, for use with [04  ], [05  ], and [06      00]
This is by no means a complete list, but it contains stuff for the beginning of the game as well as other interesting things.

Event Flags
04 02 00 = Default "Say something different" flag it's universal, so if it's set for one person, it's set for everybody.
04 0B 00 = Enemies will appear!
04 7A 02 = Paula is captured by Carpainter, and begins calling Ness telepathically.
04 CB 00 = Set after you learn the Stoic Club’s phone number
04 D6 01 = Tracy says something different right after the beginning
04 D7 01 = Mom doesn't bother you about getting dressed at the beginning.
04 D8 01 = Text changes after you talk to Pokey on the hill.
04 DA 01 = Mom appears outside the front door.
04 ED 02 = Wears normal clothes instead of pajamas.
04 EE 02 = Triggers Mom's message when you run out of the house before talking to her.
04 EF 02 = During Chaos Theater concert, the people will vanish.  (Certain sprite problems arise if they don't.)
04 49 00 = Signals the end-game conditions after Giygas is gone.

// Your Sanctuary
04 BE 00 = Set after Titanic Ant is defeated
04 BF 00 = Set after Mondo Mole is defeated
04 C0 00 = Set after Trillionage Sprout is defeated
04 C1 00 = Set after Shrooom! is defeated
04 C2 00 = Set after Plague Rat of Doom is defeated
04 C3 00 = Set after Thunder and Storm are defeated
04 C4 00 = Set after Electro Specter is defeated
04 C5 00 = Set after Carbon Dog and Diamond Dog are defeated
 

// Triggered when Frank is defeated
04 40 00 - Guard will let you pass to see Pirkle.  Base "Frank is dead" event
04 B9 02 - Not text-based, whatever the frell it is.  Maybe to keep Frankystein sprite away.

04 6B 01 - Affects one Shark - "@Who are you talking to?"  ...WTF?
04 6C 01 - Ditto affect to the other Shark...  freakin' weird.
05 6D 01 - DITTO to first Shark inside...  But it unsets it.  It's set after he gets wasted.
 

// Triggered when Titanic Ant is defeated
04 BE 00 - Set after Titanic Ant is defeated - I dunno.
04 B6 00 - Basic "Been there, done that."  Strong is ready to take you in.
04 24 00 - Cop shows up.  Automatically unsets when you see him.
04 C1 01 - Unknown... ---------------------------|___May be Captain Strong
04 C2 01 - Unknown, but unset after Cop Fight ---|
04 26 00 - I dunno.

// Cop Stuff
04 27 00 - Cop is waiting at the station
05 26 00 05 27 00 - Unset cops?
05 21 01 05 22 01 05 23 01 05 24 01 05 25 01 - Unset... something... - done when Strong takes you to the back room

// Triggered when Captain Strong is defeated
04 69 00 - Basic "Strong got wasted" code.
05 C2 01 - See above.
05 23 00 - Unknown.

// These codes are set when you pick up Picky.  Notice 25 00 has something to do with the Cop Fight as well...
05 25 00 = ?
05 E6 02 = ?

// Here's a short list by michael_cayer that overviews present boxes.  If the flag is set, the box is open already.  Refill it with [05  ]!

ONETT & GIANT STEP:

04 20 03 - Onett hilltop. (Bread roll)
04 21 03 - Garbage can next to Burger Shop. (Hamburger)
04 22 03 - Box on route from Onett to Twoson. (Hamburger)
04 23 03 - Trash can east of Hotel. (Empty)
04 24 03 - Trash can next to Arcade (guarded by a Shark). (Can of fruit juice)
04 25 03 - Box in Tracy's room. (Cracked bat, of course!)
04 26 03 - Third box in the Giant Step caves (closest to the Titanic Ant). (Hamburger)
04 27 03 - First box in the Giant Step caves (closest to the shack). (Skip Sandwich)
04 28 03 - Second box in the Giant Step caves. (Cold Remedy)

TWOSON:

04 29 03 - Box on the side of the road connecting Twoson and Threed. (Skip Sandwich)
04 2A 03 - Box in Paula's room at the Preschool. (Teddy Bear)
04 2B 03 - Trash can in Apple Kid's house. (Broken Machine)

HHV:

04 2C 03 - Box in the HH-HQ.  (Croissant?)
04 2D 03 - Another box in the HH-HQ. (Skip Sandwich?)

PRV:

04 2E 03 - Box east of the busted bridge. (Luck Capsule)
04 2F 03 - Box north of the pencil statue. (Hard Hat)
04 30 03 - ???
04 31 03 - Box east of the pencil statue. (Travel Charm)
04 32 03 - ???
04 33 03 - Box south of the entrance to the cave that leads to HHV. (Cup of Lifenoodles)

LILLIPUT STEPS:

04 34 03 - Box by Mondo Mole? (PSI Caramel?)
04 35 03 - Box south of entrance. (Great Charm)
04 36 03 - Box to the far east of the entrance. (Croissant)