My Favourites are:
1) Financial: Helps build a very strong economy and tech like crazy. If your running CE, your laughing.
2) Industrious: I'm generally a peaceful player, and like building wonders and looking for cultural victories, so this helps me get those wonders quicker. Huayna Capac is my favourite leader, so it's hardly suprising to see this as my second favourite trait.
3) Organized: Makes building a larger empire easier early on, due to reduced civic costs, and cheap courthouses.
4) Charismatic: If you have little to no luxury resources, this can eleviate that early unhappiness, and allows you to whip a little more then normal. And thats not forgetting the reduced cost of unit promotions.
5) Creative: Allows you to skip monuments and concentrate on other improvements. Cheap libraries are also nice.
6) Spiritual: I hate anarchy, especially if it lasts more then one turn. Avoiding this can make often make the difference between founding a religion or building a wonder, or missing out altogether.
7) Philisophical: I don't use an SE, otherwise, this would be higher. Still, it's nice to have quicker Great People.
8) Expansive: The health bonus is great if you don't get many health resoucres, or your cities have a lot of jungle or flood plain tiles around.
9) Aggressive: The cheap barracks are nice, as is the Combat 1 promotion. It's just that since Charismatic was added, it doesn't seem as appealing.
10) Imperialstic: The bonuses are nice, but for me at least, they contradict don't work too well together. If your looking to build peacefully, the settler bonus is good, but the GG bonus is little use, whilst if you want to expand via war, the GG bonus is great, whilst the settler bonus is far less useful. To me it seems only as if you are using half the trait. Better as a support trait.
11) Protective: Drill 1 and City Garrison 1 are really good, but the walls and castle bonus aren't particularly exciting. Again, it's a decent trait, but it's better as a support to a much stronger trait.
Ironically, Charlemagne is one of my favoutie leaders, despite his two traits being the bottom of my list, though that is almost entirley due to the strength of the Rathuas.