Sta.sh
There are many concerns about episode chronology when considering season one as a whole. There are a bunch of monsters at the start of the season, while the CMC take over during the second half. The first half is pretty AJ/RD/PP heavy, while the last half is overloaded with Rarity and Fluttershy. The Gala episode has an Everyone Laughs ending, but to me it feels tacked on and anti-climactic, and doesn't work as a season finale as well as Cutie Mark Crusaders would. (S2 update: we now know the Discord episodes were produced as the season/series finale.)
If we take the air order as the chronological order:
episodes 1-10 summer/fall, year 1000 of the Summer Sun Celebration
11 Winter Wrap-Up 1001
12 Call Of The Cutie 1001
13 Fall Weather Friends 1001
14-26: spring/summer 1002
This means the mane 6 got their tickets right after saving Equestria from Nightmare Moon, then 1 3/4 years later they go to the Gala. Season 2 update: Although a royal ball may have a waiting list that far in advance, air chronology is also impossible because Secret of my Excess is focused around Spike's first Ponyville birthday.
This is my attempt to fix unbalancing issues and chronological flaws. The season is re-ordered with these factors in mind:
- breaking up mane 6/monster/CMC clumps
- post-pilot episodes featuring most of mane 6 before Ticket Master turns them into selfish parodies of themselves
- putting bulk of apple-harvesting episodes pre-Applebuck Season
- mini-arcs of episodes that work well together
So here it is:
(revised 5/31/12)
Summer/Fall 1000:
01 - Mare In The Moon
02 - Elements of Harmony
08 - Look Before You Sleep
09 - Bridle Gossip
07 - Dragonshy
03 - The Ticket Master
10 - Swarm of the Century
16 - Sonic Rainboom
05 - Griffon The Brush-Off
20 - Green Isn't Your Color
06 - Boast Busters
12 - Call of the Cutie
04 - Applebuck Season
15 - Feeling Pinkie Keen
13 - Fall Weather Friends
30 - Luna Eclipsed (season 2)
Spring 1001:
11 - Winter Wrap Up
17 - Stare Master
24 - Owl's Well That Ends Well
14 - Suited for Success
22 - A Bird in the Hoof
26 - The Best Night Ever
21 - Over a Barrel
25 - Party of One
18 - Show Stoppers
19 - A Dog and Pony Show
23 - The Cutie Mark Chronicles
The reversal of Sonic Rainboom and Griffon The Brush-Off is something many have commented on:
Pinkie Pie: Hoof-biting action overload! She was like a stunt superstar, flying higher and higher, and then Rainbow Dash swooped down--swoosh--and right before she hit the ground--shoom-she pulled up--rrrmmm!
Twilight Sparkle: Uh-huh.
Pinkie Pie: And then she looped around and around like fwoom fwoom fwoom fwoom fwoom fwoom fwoom!
(The fwoom fwoom fwoom at the end doesn't match, but everything right before matches perfectly, although it could also describe any diving stunt. She's Pinkie Pie, yet some accept her excited noises as exact canon for some reason.)
Mini-arcs:
Sonic Rainboom/Griffon The Brush-Off: Pinkie Pie describes Rainbow Dash
Applebuck/Pinkie Keen/FWF/Luna Eclipsed/WWU: seasonal changeover is unavoidably the bulk of Applejack-heavy episodes in the season, so I broke it up.
Suited/Bird/Best Night Ever: Fluttershy may be helping Rarity make the dozen of each dress for Hoity Toity, which is why she looks through a rack of them in her home in A Bird In The Hoof
Over A Barrel/Party of One: Pinkie's least effective song is followed by her least effective party invitations
Season 2's Luna Eclipsed fits thematically in the fall following Luna's return, and Twilight pens the letter, so it need not follow Lesson Zero.
Let me know if you see anything clearly out of order. Apples and Gala dresses don't count; this show was not made to withstand logic hammering, per Lauren. And please let me know if this enhances (or detracts from) your viewing experience.
Cheerful 
