Below is a list of general readings that I think it would be especially valuable for graduate students in my lab to read (especially while studying for comprehensive exams). This is by no means a complete list, and it does not provide any attempt to include specialized papers for individuals. It is also just a preliminary pass … the list will grow over time (suggested additions welcome).
Begon, M., C.R. Townsend, and J. L. Harper. 2006. Ecology: From Individuals to Ecosystems, Fourth Edition. Blackwell. [Probably any of the major advanced ecology text books will give adequate background for comprehensive exams … this just happens to be my favourite.]
Gilovich, T. 1993. How We Know What Isn't So. Free Press. [This is a psychology book, and is not directly relevant to our field .. but it provides a lot of really interesting stuff about how people think and evaluate evidence, and has become something that I think every scientist should read.]
Gill, F.B. 1995. Ornithology, Second Edition. Freeman and Co. [This is the best single overview of the science of ornithology. A third edition is rumoured to be out soon. Again, something to use to study for comps.]
Martin, P., and P. Bateson. 1993. Measuring behavior: an introductory guide, Second Edition. Cambridge University Press. [If you plan to do any behavioural sampling you should look at this book first.]
Real, L.A., and J.H. Brown (eds.) 1991. Foundations of Ecology: Classic Papers with Commentaries. University of Chicago Press. [This book gives a good canned history of the field of ecology. The overview essays for each section were particularly useful to me when studying for my comprehensive exams as an graduate student.]
Sutherland, W. J. 1996. From individual behavior to population ecology. Oxford University Press, Oxford, United Kingdom. [This book may not be relevant to everyone, but I find it helpful for thinking about the link between behavior and populations.]
Caughley, G. 1994. Directions in conservation biology. Journal of Animal Ecology 63: 215-244. [An historically very important review.]
Ellison, A. M. 1996. An introduction to bayesian inference for ecological research and environmental decision-making. Ecological Applications 6: 1036-1046.
Hurlbert, S.H. 1984. Pseudoreplication and the design of ecological field experiments. Ecological Monographs 54:187-211. [Read this annually.]
MacNab, J. 1984. Wildlife managment as scientific experimentation. Wildlife Society Bulletin 11: 397-401.
Rice, W.R. 1989. Analyzing tables of statistical tests. Evolution, 43, 223-225. [A key statistics paper.]
Stephens, P.A., S.W. Buskirk, G.D. Hayward, and C. Martinez del Rio. 2005. Information theory and hypothesis testing: a call for pluralism. Journal of Applied Ecology 42: 4-12.
Sutherland, W.J. 2006. Predicting the ecological consequences of environmental change: a review of the methods. Journal of Applied Ecology 43: 599-616. [This recent article has a nice summary of the general approaches that people take to apply ecology.]
Van Horne, B. 1983. Density as a misleading indicator of habitat quality. Journal of Wildlife Management 47:893-901.