[Crystal_Ageha]

Okay, I quickly made up a fairly accurate list of how many songs have had how many remixes.
I included every remix album, including MY STORY CLASSICAL. I did NOT include singles (since almost all the remixes on singles are also on albums; however, to make it more accurate, I would say to add a few numbers to songs from the first and second albums, specifically Depend on you, Boys & Girls, appears and Fly high) or mega mixes aside from the ones specifically formed into an album (for example, I did not include the mega mix on the S/S~LiA~ single). I also did not include the unreleased versions of ayu-mi-x 6.
Here's the list:

A Song for XX - 4
A Song is Born - 1
About You - 1
alterna - 1
And Then - 6
appears - 10
As if... - 2
AUDIENCE - 6
Beautiful Fighters - 1
BLUE BIRD - 1
Boys & Girls - 12
CAROLS - 2
Catcher in the Light - 1
Close to You - 1
Connected - 2
Daybreak - 3
Dearest - 6
Decision - 1
Depend on you - 5
Dolls - 2
Duty - 4
End of the World - 2
End roll - 6
Endless sorrow - 4
ever free - 1
Everlasting Dream - 1
everywhere nowhere - 3
evolution - 4
Far Away - 7
fated - 1
flower garden - 1
Fly high - 14
For My Dear... - 1
Free & Easy - 3
FRIEND II - 1
from your letter - 2
GAME - 2
girlish - 3
glitter - 1
Greatful Days - 1
Hana - 3
HANABI - 5
Happy Ending - 2
Heartplace - 3
HEAVEN - 1
HONEY - 1
HOPE or PAIN - 1
I am... - 4
immature - 7
independent - 4
INSPIRE - 1
JEWEL - 1
July 1st - 4
Kaleidoscope - 1
kanariya - 8
Key - 2
Ladies Night - 1
M - 5
Moments - 2
monochrome - 5
Naturally - 3
NEVER EVER - 4
No More Words - 1
No way to say - 1
ourselves - 1
Over - 1
part of Me - 1
poker face - 3
POWDER SNOW - 2
Prologue - 2
P.S II - 2
Real me - 3
SCAR - 2
SEASONS - 7
SIGNAL - 2
Startin' - 1
Starting Over - 1
STEP you - 1
still alone - 3
SURREAL - 9
talkin' 2 myself - 1
teddy bear - 1
TO BE - 4
Together When... - 1
too late - 5
Trauma - 8
Trust - 2
Two of Us - 1
UNITE! - 5
vogue - 4
Voyage - 4
walking proud - 2
WE WISH - 3
WHATEVER - 5
Who... - 7
winding road - 1
Wishing - 2
Wonderland - 1
YOU - 4


Fly high definitely wins, and Boys & Girls is a close second. Other big ones include appears, Far Away, immature, kanariya, SEASONS, SURREAL, Trauma, and Who...