Well, as Zaarin said, all of the themes are exquisite, and some of them being at the bottom doesn't mean that they're bad by me. I think my list would be this right now:
1.Byzantium
The high expectations I went in with by the Byzantine soundtrack were more than fulfilled. Epic ever since the first tones of the ancient theme, with the lyre having its fine charm as well. Fine medieval. An absolutely wonderful industrial, filling me with somewhat sacred feeling at the beginning, as well as portraying fine picture of the Imperial Byzantine glory - like a picture of fully packed hippodrome of Constantinople cheering its Emperor in his triumph. And there is just something that always gets me by that serene eight second long trumpet segment at the end of the theme. I really don't know why, but I find it to be an absolutely magical touch.
Byzantines also get a bonus point for having a good atomic as well - I am one of the folks who do not like atomics most of the time

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2. Gaul
The Gallic themes are something wonderful. A simple, yet beautiful melody. The carnyx and the lyre of the ancient and medieval themes manage to paint a beautiful picture of a Gallic settlement in antiquity. And then comes industrial, and completely changes the picture by its tone. From idylic settlement, right onto a battlefield. The industrial manages to beautifully conserve the feel of atiquity, and it does indeed sound like a music that would play in an epic scene where the Gauls march and engage a Roman legion. It is heroic, it is strong, emotive, beautiful and fierce. The atomic theme isn't bad - it actually sounds quite good, but it does break the touch of antiquity that the industrial managed to preserve in itself.
3. Portugal
A very young theme which will yet have to find its proper place on this list, but I think number three is a safe place for now. Pleasant, if a bit too short ancient. A great medieval with the Portuguese guitar and the medieval strings forming a fine pair. The industrial theme is a matter of pure beauty to my ears, deeper explanation of why you can read on the previous page of this thread because I'm too lazy to write it up again

. Unfortunately, the atomic theme is not exactly a very fine one - the slow, but steady, dance-like buildup and execution of the industrial is perfect as it is, and the supporting percussion is more disruptive to that then enhancing.
4. Babylon
Very much unlike the Civ V peace theme, this is a theme that finally managed to portray the magnificence of the wondrous ancient city of Babylon, especially by its industrial version. I have come to like this theme's measuredness, building epically up into magnificent and epic triumph, especially. I even grew to like the medieval version in the end. Babylon also impressed me by being another civ with an atomic theme that I ended up liking

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5. Ethiopia
Ethiopia is a rare one by me. I have mentioned earlier that I don't like medievals that much, and that industrials are my preferred themes. Ethiopian medieval theme managed to simply impress and touch me with its sheer warmness and beauty provided by the combination of the voices, flute and the lovely string instrument, and the industrial/atomic theme opening nearly reaches the beauty of the Malian one, my current favourite opening of any theme in this game.
6. Gran Colombia
I remember being very excited over this one when it came out. The exquisite pajarillo part by the medieval had me excited the first time I listened to it and I still love it, and the cello, the boldness and the beautiful opening of the industrial ensured that it was my favourite single theme of the pack till today Portuguese release. Anyway, either repetiton did its thing, or maybe the others were just better to my ears - overall, the theme ends sixth on my list

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7. Maya
It is a beautiful and joyful theme, and I simply adore the magnificent opening of the industrial/atomic version - I like to stay at LSS' diplo screen until that part ends, simply because how powerful and unique it feels.
8. Vietnam
It is an amazing, fiery and lively theme in its own right, with fine heroic feel. If one closes their eyes and lets the music help them paint a picture in their imagination, he can end with the theme providing them with an explosion of images. Sometimes, the themes can feel like too much though, especially by the last two versions, and even the first two can sometimes feel a tad too sharp to ear.