Since being on my anti-depressant, effexor, I have been struggling with puffy eyes and/or dark circles practically every morning. Nothing in my diet has changed, and if anything, I have increased nutrient and vitamin content in my diet. Also, I have been getting much more sleep that is much deeper than usual (by that I mean that I have regularly had dreams, therefore indicating I've been in REM a lot which is the key to getting good sleep). So, in my case, I have been negating all of the mentioned causes.
I have often wondered about them as well, and don't really have any more ideas of what causes them, except maybe being on certain medications and/or experiencing more REM sleep.