A couple of years ago now the Journal of Applied Ecology had an interesting article entitled:
The identification of 100 ecological questions of high policy relevance in the UK. Ecologists wanted the list to have a major impact on both science and policy and in the press release they liken the list to the 23 mathematical problems David Hilbert posed at the Second International Congress of Mathematicians in Paris in 1900. This list had a major impact on mathematics throughout the twentieth century.
The list is interesting to browse through (the link above takes you to the complete paper) because it really does help to highlight how little we know in ecology. It is also interesting to speculate what fraction of the questions will have general answers and what fraction will have answers that vary from system to system.
Although a few questions are rather UK specific most are equally relevant to the US.