I went knowledge and order.
Knowledge's science boost is too good to ignore in most cases (especially the 20% while happy boost), and Order's providing of a great engineer (plus another through faith building in most cases) is a huge plus.
Liberty/Tradition - Generally I pick one or the other, though I have gone both at times.
Honor - My least chosen, generally I want tradition or liberty.
Piety - Culture wins only, though I will admit the +1 happy for shrines and temples looks really tempting in general.
Commerce - It has some great bonuses now, if I was going to pick a third tree as an always pick it would be this one.
Freedom - Also has some decent bonuses, the temptation is growing.
Nationalism - Never touch it in most cases, especially since it conflicts with freedom.