I went thru the same dilemma - in the end I chose to order by brand, then by colour within each brand. Organizing by colour only just looked too haphazard with all the different bottle shapes mixed up together
I'd go by seasons. I often feel like wearing a vamp/a bright, and then it helps to have them all together
Thank you for the suggestions. I think I will have some time this weekend to sort it out. Right now I am using a rectangle hat box (of sorts). I can double stack NP in it since it is kind of tall, so I have the 2nd row of NP in small little baskets. I think I may have to line the bottom row with shorter nail polish bottles. I love these kind of organization projects!