Title:           Recommended Reading Order (Updated 6/16)
Author:          TheScooter
Pastebin link:   http://pastebin.com/CFPUUM1T
First Edit:      Thursday 10th of May 2012 06:03:31 AM CDT
Last Edit:       Thursday 10th of May 2012 06:03:31 AM CDT

I know this Pastebin is a mess, so here's a comprehensive list of the fics and their recommended order. Will keep this updated as I post on the Pastebin.
 
1) Prequel of Sorts
2) Sympathy for Scootaloo Prologue through Pt. 6
3) When Friends Change
4) Family is Relative
5) Birds and Bees
6) Hurricane Fluttershy Featuring AnonDad
7) Ponyville Confidential Featuring AnonDad
8) Climate of Change Pt. 1-4
9) When You're Gone?
10) Mistake of Passion
11) A Nightmare Defense
12) A Domestic Situation
13) Knight Rise
14) A Knight in Shining Armor
15) Siege of Trottingham
16) Time After Time
17) Smile
18) Just One More
19) Hurricane Scootaloo
20) Dad's Nightmare
21) Nopony Doesn't Like Cheerilee
22) Friend and Family Affair
23) Cherry Poppin Daddy (AnonxCheerilee NSFW)
24) Stepping in
25) Stronger Addictions
26) Dry Break
27) Breaking up is Hard to do
28) Home Sprints
29) In the Light of a New Morning
30) Scootaloo Taken
31) Pony Fluff (Not to be confused with Fluffy Pony)
32) Blue Box, Pink Party
33) Another Time
34) A Canterlot Wedding Pt. 1 & 2
35) The Other Family
36) Two Dinners
37) Angel Cake (Doctor Whooves fic)
38) The Master of Chaos
39) Losing Control
40) Star Song Refrain Pt. 1 & 2
41) Apologies, Amends, and New Beginnings
42) All on the Table
43) Operation Rolling Thunder
44) Apple Pieces
45) Head in the Clouds
46) Hearts n' Hooves Day
47) Pendant of Nobility
48) Campy Fun
49) Game Night
50) Meet Snips' Mother
 
Somewhat non-canon, but still good: For Old Times Sake