(In order by date. Being on this list does not make it recommended reading.)
1 My Little Dashie
2 Rainbow in the Dark
3 But the Kitchen Sink
4 Reading Rainbow
5 I Almost Lost Everything
6 Brony Hero of Equestria
7 You In Equestria
8 MLD: A Sequel
9 MLD: A Threequel
10 The Brony International Guard
11 Anthropology
12 Arrow 18 Mission Logs
13 Quantum Castaways
14 The Pony in My Pocket
15 Cuddling Ensues
16 Keeping Your Hooves on the Ground
17 My Little Stashie
18 The Roommate
19 Why am I Pinkie Pie?
20 Pinkie Watches Paint Dry
21 Truth vs. Fiction
22 Read it and Sneak
23 Running From Twilight
24 The Brony Guard Unlimited
25 Sunny Skies All Day Long
26 Background Pony
27 The AAA of Tank the Tortoise
28 Biblical Monsters
29 Please Proof Me!
30 What Dreams May Come
31 Lyra and the Hand of Man
32 Faith
33 I Met a Pony in Hell
34 The Conversion Bureau
35 Rainbow Dash Does Something Ironic
36 To the Wind
37 Portal to Another World
38 Fluttershy Has Tea with Jesus
39 Written in Dust
40 Hammin' in Equestria (Working link)
41 Live the Rainbow
42 Dash's Tears in the Rain
43 In Our World - Kindness
44 Hello, Sedna
45 The Not So Odd Outcast
46 Project: Sunflower
47 Friendship is Optimal
48 My Little Person: Lyle Hartman
49 When I Was Thirty
50 The Envelope
51 Off the Edge of the Map
52 An Earth Pony's Guide to Magic
53 Theory
54 Memory Pending
55 The Incredibly Epic WIns of Winbow Dash
56 Equestria from Dust
57 Unfamiliar Skin
58 Article 2
59 The Numbers Don't Lie
60 Hiccups
61 No, I Am NOT A Brony, GET ME OUTTA EQUESTRIA!!!
62 Them
63 Dash of Humanity
64 Twilight Makes First Contact
65 Whip and Wing
66 Stardust
67 First Contact is Magic
68 Five Score Divided by Four
69 You Do (Not) Belong
70 I.D. - That Indestructible Something
71 EITTICOASSOTMOAFOWWYL!?
72 Believing Stories
73 For Queen and Country
74 Airshipping Is Magic
75 Refraction

(Stuff that bothers me enough to write it down)

1: Cupcakes are not pastries.
2: Highest level unicorns have aging magic.
3: Winning the lottery or inheriting from a long lost relative is cliche.
3.1: If something seems too convenient to be true, it probably is.
4: "Tuna crunch" is a meat product.
5: Do not mix metric and American units together.
6: Equestrian physical laws, equations, theories, philosophies etc. should not be named directly after their equivalent human discoverers/inventors.
7: Ponies should not use leather. It creeps me out.
8: Characters not familiar with modern Equestrian culture should not immediately know how to handle Equestrian currency. Including but not limited to: Characters from far off lands (or planets), from different time periods, or from alternate dimensions/universes e.g. humans.
9: Nodding your head means yes. Shaking your head means no.
10: Do not use internet slang (wtf, omg, lol) in dialogue.
11: Intentionally witholding details about what the character is looking at makes me more annoyed than curious. It is immersion breaking if used too frequently.
12: References are nice, but don't let them derail the story.
13: Be consistent. Don't switch from limited to omniscient halfway through.
14: Place your character in their "normal" before your remove them from it.
15: Show, don't tell.