The order in the game's songs

[Kailieann]

Thanks for the tracklist!

There are the tracks I have not found in the mus directory: (11 tracks)

01. intro
04. traveller
05. home
12(10?). fatal
12. undiscoveredwaters
18. heartoftheforest
20. mothernature
23. above
25. li
30. lostwaters
41. thereturn

And there are the tracks of the mus directory that you have not listed: (17 tracks, I excluded tracks 'test.ogg' and 'superflyremix.ogg' as they're not in the game)

arboreal
bblogo
bigboss
flyaway
forestgod
inevitable
licave
lucien
mithalaanger
mithalaend
mithalapeace
openwaters
openwaters2
openwaters3
theend
veil
youth

Weren't there some changes in the songs names? And for instance, hasn't 'worship' been splitted? (There is 5 tracks called worshipX.ogg in the 'mus' dir, corresponding to the 5 shapes of the final boss)

"Prelude" is the last track??

Intro is probably naija_intro-music from the vox folder
Traveller is openwaters
Home is youth
Undiscovered Waters is openwaters3
Heart of the Forest would be arboreal
Mother Nature is forestgod
Above is probably veil
Li is almost certainly licave
The Return would be theend

Fatal is probably bigboss
Lost Waters I'm guessing is openwaters2

Mithala (track 16) probably includes anger/end/peace

That just leaves inevitable, lucien, and flyaway, which are still conspicuous by their absence.

Lucien and flyaway are at least somewhat understandable. Inevitable.. I don't actually remember it from the game, which makes it hard to place (I'm sure it was in there, I just don't remember when)

[Limestraël]

Okay! So this gives us:

01 naija_intro-music (intro)
02 title
03 light
04 openwaters (travellers)
05 youth (home)
06 cave
07 mystery
08 ancienttest
09 archaic
10 bigboss (fatal)
11 marchofthekrotites
12 openwaters3 (undiscoveredwaters)
13 miniboss
14 remains
15 cathedral
16 mithala
17 mithalaanger
18 mithalaend
19 mithalapeace
20 fallofmithalas
21 arboreal (heartoftheforest)
22 hopeofwinter
23 forestgod (mothernature)
24 druniaddance
25 brightwaters
26 veil (above)
27 moment
28 licave (li)
29 suntemple
30 sunwormcave
31 sunworm
32 prometheus
33 openwaters2 (lostwaters)
34 seahorse
35 abyss
36 gullet
37 icywaters
38 sunkencity
39 sunken
40 thebody
41 fallenbreed
42 worship1
43 worship2
44 worship3
45 worship4
46 worship5
47 endingpart1
48 theend (thereturn)
49 losttothewaves
50 prelude

And you're right, this leaves us inevitable, lucien, and flyaway.
Any idea where they're to be put? (I do not remember where they're exactly in the game)
And I still find weird that "Prelude" should be put at the end...

[Align]

Lucien is heard in both the beginning and end IIRC; I put it after 'title'. Hum, no it's not, it's only in towards the end. I confused it with the music heard in vox\naija_intro-music.ogg. I think it's just before Fly Away, then.
Inevitable is heard when the King Jellyfish (?) closes in on you in that one room in the Abyss.
Flyaway... well, it's definitely after The Return, but I'm not sure if Lost to the Waves comes before it as well.
(also mithalaend should come just before Fall of Mithalas)

[Nava]

That's the official CD then?

No it's the unofficial CD, since he hasn't completed the project. If he does decide to go ahead with making a physical soundtrack, the song order might change a bit. Who knows! But glad you guys are sorting out all the discrepancies.

[Limestraël]

Well, well, well...

This could be like it:

01_Naija_Intro-music.ogg
02_Title.ogg
03_Light.ogg
04_Open_Waters.ogg
05_Youth.ogg
06_Cave.ogg
07_Mystery.ogg
08_Ancient_Test.ogg
09_Archaic.ogg
10_Big_Boss.ogg
11_March_Of_The_Krotites.ogg
12_Open_Waters_3.ogg
13_Miniboss.ogg
14_Remains.ogg
15_Cathedral.ogg
16_Mithala.ogg
17_Mithala_Anger.ogg
18_Mithala_Peace.ogg
19_Mithala_End.ogg
20_Fall_Of_Mithalas.ogg
21_Arboreal.ogg
22_Hope_Of_Winter.ogg
23_Forest_God.ogg
24_Druniad_Dance.ogg
25_Bright_Waters.ogg
26_Veil.ogg
27_Moment.ogg
28_Li_Cave.ogg
29_Sun_Temple.ogg
30_Sun_Worm_Cave.ogg
31_Sun_Worm.ogg
32_Prometheus.ogg
33_Open_Waters_2.ogg
34_Seahorse.ogg
35_Abyss.ogg
36_Gullet.ogg
37_Icy_Waters.ogg
38_Sunken_City.ogg
39_Sunken.ogg
40_The_Body.ogg
41_Fallen_Breed.ogg
42_Worship_1.ogg
43_Worship_2.ogg
44_Worship_3.ogg
45_Worship_4.ogg
46_Worship_5.ogg
47_Ending_Part_1.ogg
48_The_End.ogg
49_Lucien.ogg
50_Fly_Away.ogg
51_Lost_To_The_Waves.ogg
52_Prelude.ogg

I'd put 'Inevitable' at position 37, right between 'Gullet' and 'Icy Waters', do you agree?
Well, this is a bit of a tough work! 

I would also put the first songs in this order:

01_Prelude.ogg
02_Title.ogg
03_Naija_Intro-music.ogg
04_Light.ogg

since it's the order they come in during the very first part of the game.

[Kailieann]

I agree with the order for the first four, as well as the placement for Inevitable.

I'm fairly certain Lucien and Fly Away come after Lost to the Waves, though (unfortunately I can't check, since I keep accidentally saving over my endgame files).
Also, without knowing why Alec chose to have Prelude last, I'm not sure whether they would be placed before it or after.

For narrative purposes, I'd also put vox/eric.ogg between Ending Part 1 and The End.

[Limestraël]

Let's sum up again! 

(01_Prelude.ogg?)
02_Title.ogg
03_Naija_Intro-music.ogg (vox)
04_Light.ogg
05_Open_Waters.ogg
06_Youth.ogg
07_Cave.ogg
08_Mystery.ogg
09_Ancient_Test.ogg
10_Archaic.ogg
11_Big_Boss.ogg
12_March_Of_The_Krotites.ogg
13_Open_Waters_3.ogg
14_Miniboss.ogg
15_Remains.ogg
16_Cathedral.ogg
17_Mithala.ogg
18_Mithala_Anger.ogg
19_Mithala_Peace.ogg
20_Mithala_End.ogg
21_Fall_Of_Mithalas.ogg
22_Arboreal.ogg
23_Hope_Of_Winter.ogg
24_Forest_God.ogg
25_Druniad_Dance.ogg
26_Bright_Waters.ogg
27_Veil.ogg
28_Moment.ogg
29_Li_Cave.ogg
30_Sun_Temple.ogg
31_Sun_Worm_Cave.ogg
32_Sun_Worm.ogg
33_Prometheus.ogg
34_Open_Waters_2.ogg
35_Seahorse.ogg
36_Abyss.ogg
37_Gullet.ogg
38_Inevitable.ogg
39_Icy_Waters.ogg
40_Sunken_City.ogg
41_Sunken.ogg
42_The_Body.ogg
43_Fallen_Breed.ogg
44_Worship_1.ogg
45_Worship_2.ogg
46_Worship_3.ogg
47_Worship_4.ogg
48_Worship_5.ogg
49_Ending_Part_1.ogg
50_Eric.ogg (vox)
51_The_End.ogg
52_Lost_To_The_Waves.ogg
53_Lucien.ogg
54_Fly_Away.ogg

Thank you all for your participation, by the way! 

[Align]

Prelude is definitely at the very end.
Moment and Li_cave should be swapped if we're going with the in-game order, since Moment is when they kiss, and you're in the cave before that...
Then there's vox/title3.ogg, which you hear just before the Title music starts up if you go through the intro.
I'd put them like this (after some renaming, hopefully its clear which are which)