When it comes to just plain neatness id have to say the Star Wars II mod, it has a horibble AI (wasnt made for solo play).
Emperor Fritsch the Mentally Challenged
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i came i saw.....i forgot where i put my sandwich
They are in alphabetical order for me (V 2.21). I gather the only other sorting making sense would be by modification/creation date, and I seem to recall the previous Version I used work that way, but don't quote me on that.
You can place a character such as '_' at the beginning of the folder names for the mods you want to appear at the top. This should cause them to appear at the beginning of the list.