(from my blog post)
I’ve been a bad brony. I haven’t even read the comics yet.

In order to seek redemption for my transgression, I’ve set myself on a journey to read them all. However, I want to do it the right way—in the canon chronological order (assuming there is such a thing as canon chronology order to them).

Here lies my ordeal. In order for me to order them in the correct order, I’d have to read them unorderly first in order to order them in the correct order and that’s a tall order to fill, as I would be doing it out of order. I just want some order in my readings.

I ask those of you, that have already read them, to help me set them up in the canon chronological arrangement for reading (the most distant one in the past first; the most recent one (or future one) last). Also, let me know if I missed any. I will edit this list according to the suggestions from the comments. Here is the approximation of the canon chronology that still needs some tweaking (that’s where you come in):

PRESEASON 1
My Little Pony: The Journal of the Two Sisters: The Official Chronicles of Princesses Celestia and Luna (technically not a comic, but I’m going to read it anyway).
(released on 2014.06.10)

My Little Pony - Friendship is Magic 11 (Shining Armor and Cadence - “Neigh Anything”)
(2013.09.24)

My Little Pony - Friendship is Magic 12 (Shining Armor and Cadence - “Neigh Anything”)
(2013.10.30)

My Little Pony Annual 2013 Equestria girls (The Fall of Sunset Shimmer (set in Equestria))
(2013.10.30)
END PRESEASON 1

SEASON 1
The Magic Begins
(released on 2013.08.27)
END SEASON 1

My Little Pony - Friendship is Magic 05 (Nightmare Rarity)
(2013.03.27)

My Little Pony - Friendship is Magic 06 (Nightmare Rarity)
(2013.04.24)

My Little Pony - Friendship is Magic 07 (Nightmare Rarity)
(2013.05.16)

My Little Pony - Friendship is Magic 08 (Nightmare Rarity)
(2013.06.13)

SEASON 2
END SEASON 2

My Little Pony - Friendship is Magic 01 (The Return of Queen Chrysalis)
(also titled as How Much Is that Pony In The Window, I think)
(2012.11.28)

My Little Pony - Friendship is Magic 02 (The Return of Queen Chrysalis)
(2013.01.02)

My Little Pony - Friendship is Magic 03 (The Return of Queen Chrysalis)
(2013.01.30)

My Little Pony - Friendship is Magic 04 (The Return of Queen Chrysalis)
(2013.03.06)

Twilight Sparkle
(2013.02.20)

Rainbow Dash
(2013.03.20)

Rarity
(2013.04.24)

Fluttershy
(2013.05.30)

Pinkie Pie
(2013.06.20)

Applejack
(2013.07.11)

Cutie Mark Crusaders
(2013.08.22)

Princess Celestia
(2013.09.11)

Spike
(2013.11.13)

Luna
(2013.12.18)

SEASON 3
My Little Pony - Friendship is Magic 09 (Big Mac - "Zen and the Art of Gazebo Repair")
(2013.07.31)

My Little Pony - Friendship is Magic 10 (Big Mac - "Zen and the Art of Gazebo Repair")
(2013.08.28)
END SEASON 3

My Little Pony: Twilight Sparkle and the Crystal Heart Spell (novel) [has to be after the Third Season Finale, and possibly before EG]
(2013.02)

EQUESTRIA GIRLS
My Little Pony: Equestria Girls: Through the Mirror (novel)
(2013.10.01)
END EQUESTRIA GIRLS

My Little Pony - Friendship is Magic 13 (My Little Pirate: Friendship Ahoy)
(2013.11.20)

My Little Pony - Friendship is Magic 14 (My Little Pirate: Friendship Ahoy)
(2013.12.18)

My Little Pony - Friendship is Magic 17 (Reflections)
(2014.03.18)

My Little Pony - Friendship is Magic 18 (Reflections)
(2014.04.30)

My Little Pony - Friendship is Magic 19 (Reflections)
(2014.05.28)

My Little Pony - Friendship is Magic 20 (Reflections)
(2014.06.25)

My Little Pony - Friends Forever 1
(2014.01.22)

My Little Pony - Friends Forever 2 (Discord and the CMC)
(2014.02.26)

My Little Pony - Friends Forever 3 (Spike and Celestia)
(2014.03.12)

My Little Pony - Friends Forever 4 (Twilight and Shining Armor)
(2014.04.09)

My Little Pony - Friends Forever 5 (Fluttershy and Zecora)
(2014.05.21)

My Little Pony - Friends Forever 6 (Trixie and Rainbow Dash)
(2014.06.18)

My Little Pony - Friends Forever 7
(2014.07.23)

My Little Pony - Friends Forever 8
(2014.08)

My Little Pony - Friends Forever 9
(2014.09)

My Little Pony - Friends Forever 10
(2014.10)

My Little Pony - Friendship is Magic 21 (Trixie)
(2014.07.16)

My Little Pony - Friendship is Magic 22 (Trixie)
(2014.08)

SEASON 4
My Little Pony - Friendship is Magic 15 (bookworm) - [Supposedly not worth reading.]
(2014.01.14)

My Little Pony - Friendship is Magic 16 (bookworm) - [Supposedly not worth reading.]
(2014.02.05)

My Little Pony: Pinkie Pie and the Rockin' Ponypalooza Party! (novel) [takes place before Maud Pie, and (possibly?) before Pinkie Pride]
(2013.07.02)

My Little Pony: Rainbow Dash and the Daring Do Double Dare (novel) [strong hint that this takes place after Daring Don't]
(2014.01.07)

My Little Pony: Rarity and the Curious Case of Charity (novel) [possibly after Simple Ways (mention of Trenderhoof), and possibly DURING Twilight Time (references to helping fillies at the library.)]
(2014.04.08)

My Little Pony: Applejack and the Honest-to-Goodness Switcheroo (novel) [Hard to say, although definitely after Pinkie Apple Pie]
(2014.07.15)

END SEASON 4

My Little Pony: Equestria Girls: Rainbow Rocks (novel) [novelization of the shorts—so sometime between EG and Rainbow Rocks]
(2014.04.08)

RAINBOW ROCKS
END RAINBOW ROCKS

48-Page Equestria Girls Holiday Special [after Rainbow Rocks since its a holiday special. I'm assuming its winter and the first movie is set during early fall and the second looks like its set not long afterwards.]
(2014.12.)

Unsorted:
My Little Pony - Friendship is Magic 23 (pets)
(2014.09)

My Little Pony - Friendship is Magic 24 (time travel)
(2014.10)

My Little Pony - Friendship is Magic 25 (The Good, the Bad and the Ponies)

My Little Pony - Friendship is Magic 26 (The Good, the Bad and the Ponies)

mini-comic of My Little Pony: Halloween Edition
(Halloween 2013)

My Little Pony Annual 2014 (Power Ponies)
(2014.09)

The Daring Do Adventure Collection (novel)
(2014.10.07)

Equestria Girls: Rainbow Rocks - The Mane Event (novel)
(2014.08.07)

My Little Pony: Fluttershy and the Fine Furry Friends Fair (novel)
(2015.01.06)

Did I miss any comic? Does one happen in the canon timeline before another (I’m interested in the canon timeline. Release dates are irrelevant.)? How did you decide which comics to read first?

Bonus question for those that haven’t read them yet: Why haven’t you read them yet?

3586444
I have read the comics so this is the break down based on my memory its been a while since I have read some of them.

The Return of Queen Chrysalis arc issues 1,2,3 & 4 take place between seasons 2 &3.

Nightmare Rarity arc issues 5,6,7 & 8 at best maybe before season 2 but the problem is that there are continuity errors such as the episode Luna Eclipsed does contradict a few things not only that but there is a reference to season 3.

Zen and the Art of Gazebo Repair arc # 9 & 10 is pretty self contained from I recall although Trixie does show up so I think its after Magic Duel so around season 3.

Neigh Anything arc # 11 & 12 is mostly all a flashback so before season 1.

Friendship Ahoy arc # 13 & 14 and onward are after season 3 because Twilight is an Alicorn.
for the rest the comics of the main series the time lines do jump around but they are set either before season 4 or around it.

Reflections arc # 17, 18, 19 & 20 is set between seasons 3 & 4.

Book Worm arc # 15 & 16 is set during season 4.

The Trixie arc # 21 & 22 is after season 3 and also after issue 6 of Friends Forever.

That's everything about the main series that's currently out. I haven't read the Halloween issue so I can't say.

As for the Micro-series they are very self contained but since Twilight is still just a unicorn they are before the season 3 final. The Friends Forever series are also self contained but they are set after season 3 since Twilight not only has wings but Discord shows up in a two of the issues.

The Equestria Girls Annual is set before both season 1 of the show and before the movie.

3587199 Thank you, that was awesome. I'll correct my OP to incorporate the information in your comment.

It seems that I've missed some MLP novels.

My Little Pony: Twilight Sparkle and the Crystal Heart Spell (novel)
(2013.02)

My Little Pony: Pinkie Pie and the Rockin' Ponypalooza Party! (novel)
(2013.07.02)

My Little Pony: Equestria Girls: Through the Mirror (novel)
(2013.10.01)

My Little Pony: Rainbow Dash and the Daring Do Double Dare (novel)
(2014.01.07)

My Little Pony: Rarity and the Curious Case of Charity (novel)
(2014.04.08)

My Little Pony: Equestria Girls: Rainbow Rocks (novel)
(2014.04.08)

My Little Pony: Applejack and the Honest-to-Goodness Switcheroo (novel)
(2014.07.15)

The Daring Do Adventure Collection (novel)
(2014.10.07)

Equestria Girls: Rainbow Rocks - The Mane Event (novel)
(2014.08.07)

My Little Pony: Fluttershy and the Fine Furry Friends Fair (novel)
(2015.01.06)

I've added them to my OP. Did anypony read any of this? Where do they fit in canon timeline?

3611226 I've read 'em all. While theoretically they're canon, I've had a hard time reconciling them with the events of the show. If I can think of them, I'll pop in the valuable take-aways from each.

Crystal Heart Spell has to be after the Third Season Finale, and possibly before EG. Twilight's princess status is brand new to her here. Valuable take-away: Cadance's backstory. I found it a little weird and disappointing, but that's specifically been confirmed as canon by McCarthy.

The kids' books are supposed to be cumulative and read in order.

Pinkie Pie and the Rockin' Ponypalooza Party takes place somewhere in Season Four, before Maud Pie, and (possibly?) before Pinkie Pride. What confuses me is that she gives up being a party pony and attempts to be Pinkamena Serious Pie, and it feels weird that she would totally give up partying twice inside of a few months, but whatever. Valuable take-away: canon names of the Pies and a view of Pinkie's really awesome party skills.

Rainbow Dash and the Daring Do Double Dare: strong hint that this takes place after Daring Don't.

Rarity and the Curious Case of Charity: Has to be set after Rarity Takes Manehattan (Rarity gets an intern), possibly after Simple Ways (mention of Trenderhoof), and possibly DURING Twilight Time (references to helping fillies at the library.) The weird: references to Coco Cheval (although of course Coco Pommel could have been named after Coco Chanel.)

Applejack and the Honest to Goodness Switcharoo: Bonus brief sighting of Alicorn Big Mac. Hard to say, although definitely after Pinkie Apple Pie.

The Equestria Girls books: These CAN and DO change things from the movies, which I find puzzling. For example, in the movie, Twilight meets Fluttershy first, but in the book, Twilight meets Rainbow Dash first.

EG: Through the Mirror is a novelization of Equestria Girls, so immediately after Season Three.

Rainbow Rocks is a novelization of the shorts--so sometime between EG and Rainbow Rocks.

I suppose we'll find out about The Mane Event, which will probably be a tie-in with Rainbow Rocks. It's unclear how EG time works against Equestria time.

Hope that helps.