The following are what I consider important classic (>10 years ago) publications in zooplankton ecology. It is not by any means the complete reading list necessary for understanding the field of study, and it tends to reflect my own interest, which is in the area of plankton food web interactions.
Andressen, A. and D. Hessen. 1991. Carbon, nitrogen and phosphorus content of freshwater zooplankton. Limnology and Oceanography 36: 807-814.
Brooks, J.L. and S.I. Dodson. 1965. Predation, body size, and composition of plankton. Science 150: 28-35.
Dodson, S.I. 1974. Zooplankton competition and predation: an experimental test of the size-efficiency hypothesis. Ecology 55: 605-613.
Dodson, S.I. 1992. Predicting crustacean zooplankton specis richness. Limnology and Oceanography 37: 848-856.
Elser, J.J. et al. 1988. Zooplankton-mediated transitions between N and P limited algal growth. Limnology and Oceanography 33: 1-14.
Gliwicz, Z.M. 1969. Studies on the feeding of pelagic zooplankton in lakes with varying trophy. Ekologia Polska 17: 663-708.
Gillooly, J.R. and S.I. Dodson. 2000. Latitudinal patterns in the size distribution and seasonal dynamics of new world, freshwater cladocerans. Limnology and Oceanography 45: 22-30.
Gliwicz, Z.M. and W. Lampert. 1990. Food thresholds in Daphnia species in the absence and presence of blue-green filaments. Ecology 71: 691-702.
Gulati, R.D. and W.R. DeMott. 1997. The role of food quality for zooplankton: remarks on the state-of-the-art, perspectives and priorities. Freshwater Biology 38: 753-768.
Haney, J.F. and D.J. Hall. 1975. Diel vertical migration and filter-feeding activities of Daphnia. Archiv fur Hydrobiologie 75: 413-441.
Hillbricht-Ilkowska, A. 1977. Trophic relations and energy flow in pelagic plankton. Polish Ecological Studies 3: 2-98.
Lampert, W., et al. 1986. Phytoplankton control by grazing zooplankton: a study on the spring clear-water phase. Limnology and Oceanography 31: 478-490.
Lynch, M. 1977. Fitness and optimal body size in zooplankton populations. Ecology 58: 763-774.
Lynch, M. 1979. Predation, competition, and zooplankton community structure: an experimental study. Limnology and Oceanography 24: 253-272.
Pace, M.L. 1984. Zooplankton community structure, but not biomass, influences the phosphorus-chlorophyll relationship in lakes. Canadian Journal of Fisheries and Aquatic Sciences 41: 1089-1096.
Pace, M.L. 1986. An empirical analysis of zooplankton community size structure across lake trophic gradients. Limnology and Oceanography 31: 45-55.
Pace, M.L. and J.D. Orcutt. 1981. The relative importance of protozoans, rotifers and crustaceans in a freshwater zooplankton community. Limnology and Oceanography 26: 822-830.
Porter, K.G. 1977. The plant-animal interface in freshwater ecosystems. American Scientist 65: 159-170.
Riemann, B. 1985. Potential importance of fish predation and zooplankton grazing on natural populations of freshwater bacteria. Applied Environmental Microbiology 50: 187-193.
Sanders, R.W. et al. 1989. Seasonal patterns of bacterivory by flagellates, ciliates, rotifers and cladocerans in a freshwater plankton community. Limnology and Oceanography 34: 673-687.
Sherr, E.B. and B.F. Sherr. 1987. High rates of consumption of bacteria by pelagic ciliates. Nature 325: 710-711.
Sieburth, J.G., V. Smetacek and J. Lenz. 1978. Pelagic ecosystem structure: heterotrophic compartments of the plankton and their relationship to plankton size fractions. Limnology and Oceanography 34: 673-687.
The following are selected papers from the contemporary (last 10 years) literature that in my view have made important new contributions to the field. Please note again that this is quite literally just a selection, and one that is biased by my own interests in certain areas of zooplankton ecology. I will add to this list as I read new papers that appear in the zooplankton ecology literature. Some of these papers are from the coastal marine literature.
Auer, B., U. Elzer and J. Arndt. 2004. Comparison of pelagic food webs in lakes along a trophic gradient and with seasonal aspects: influence of resource and predation. Journal of Plankton Research 26: 697-709.
Hariston, N.G., Jr., A.N. Hansen and W.R. Schaffner. 2000. The effects of diapause emergence on the seasonal dynamics of a zooplankton assemblage. Freshwater Biology 45: 133-145.
Irigoien, X., K.J. Flynn and R.P. Harris. 2005. Phytoplankton blooms: a loophole in microzooplankton grazing impact? Journal of Plankton Research 27: 313-321.
Mitra, A. and K.J. Flynn. 2005. Predator-prey interactions: is ecological stoichiometry sufficient when good food goes bad? Journal of Plankton Research 27: 393-399.
Olsen, Y. et al. 2001. Comparative analysis of food webs based on flow networks: effects of nutrient supply on structure and function of coastal plankton communities. Continental Shelf Research 21: 2043-2053.
Romare, P. and L.A. Hansen. 2003. A behavioral cascade: top-predator induced behavioral shifts in planktivorous fish and zooplankton. Limnology and Oceanography 48: 1956-1964.
Sommer, U. et al. 2002. Pelagic food web configurations at different levels of nutrient richness and their implications for the ratio fish production:primary production. Hydrobiologia 484: 11-20.
Steiner, C.F. 2004. Daphnia dominance and zooplankton community structure in fishless ponds. Journal of Plankton Reseach 26: 799-810.
Here are a few of my own papers, and papers with colleagues, former students and post-docs, dealing with zooplankton ecology.
Conley, D.J., H.W. Paerl, R.W. Howarth, D.F. Boesch, S.P. Seitzinger, K.E. Havens, C. Lancelot and G.E. Likens. 2009. Controlling eutrophication: nitrogen and phosphorus. SCIENCE 323: 1014-1015.
Havens, K.E. 1992. Scale and structure in natural food webs. SCIENCE 257: 1107-1109.
Havens, K.E. 1997. Unique structural properties of plankton food webs. Oikos 78: 75-80.
Havens, K.E. 1998. Size structure and energetics in a plankton food web. Oikos 81: 346-358.
Havens, K.E. 1999. Comparative analysis of lake plankton structure vs. function. Aquatic Sciences 61: 150-167.
Havens, K.E. and R.E. Carlson. 1998. Functional complementarity in plankton communities along a gradient of acid stress. Environmental Pollution 101: 427-436.
Havens, K.E., J.R. Beaver and T.L. East. 2007. Plankton biomass partitioning in a eutrophic subtropical lake: comparison with results from temperate lake ecosystems. Journal of Plankton Research 29: 1087-1097.
Havens, K.E., T.L. East and J.R. Beaver. 2007. Zooplankton response to extreme drought in a large subtropical lake. Hydrobiologia 589: 187-198.
Havens, K.E., T.L. East, J. Marcus, P. Essex, B. Bolan, S. Raymond and J.R. Beaver. 2000. Dynamics of the exotic Daphnia lumholtzii and native macro-zooplankton in a subtropical chain-of-lakes in Florida, USA. Freshwater Biology 45: 21-32.
Havens, K.E., A.C. Elia, M.I. Taticchi and R.S. Fulton. 2009. Zooplankton-phytoplankton relationships in shallow subtropical versus temperate lakes Apopka (Florid, USA) and Trasimeno (Umbria, Italy). Hydrobiologia 628: 165-175.
Havens, K.E., B. Gu, B. Fry and K. Kendall. 2003. Stable isotope food web analysis of a large subtropical lake: alternative explanations for 15-N enrichment in pelagic vs. littoral fisheries. TheScientificWorld Journal 3: 613-622.
Havens, K.E., K.A. Work and T.L. East. 2000. Relative efficiencies of carbon transfer from bacteria and algae to zooplankton in a subtropical lake. Journal of Plankton Research 22: 1801-1809. (pdf)
Pinto-Coelho, R., B. Pinel-Alloul and K.E. Havens. 2005. Crustacean zooplankton in lakes and reservoirs of temperate and tropical regions: variation with trophic status. Canadian Journal of Fisheries and Aquatic Sciences 62: 348-361. (pdf)
Work, K.A. and K.E. Havens. 2003. Zooplankton grazing on bacteria and cyanobacteria in a eutrophic lake. Journal of Plankton Research 25: 1301-1307. (pdf)
Work, K.E., K.E. Havens, B. Sharfstein and T.L. East. 2005. How important is bacterial carbon to planktonic grazers in a turbid subtropical lake? Journal of Plankton Research 27: 357-372. (pdf)