The Rundom software citations in books and research papers (sorted by year):

2008

Stiver K.A, Fitzpatrick J.L., Desjardins J.K., Neff B.D., Quinn J.S. & Balshine S. 2008. The role of genetic relatedness among social mates in a cooperative breeder. Behavioral Ecology, doi:10.1093/beheco/arn031.
(Rundom Projects 2.0 LITE)

2007

Bakus, G.J., 2007. Quantitative Analysis of Marine Biological Communities. Wiley, 435 pp.
(Rundom Projects 2.0 LITE)

Genner M.J., Todd J.A., Michel E., Erpenbeck D., Jimoh A., Joyce Andrzej.A., Piechotki A. & Pointier J.-P. 2007. Amassing diversity in an ancient lake: evolution of a morphologically diverse parthenogenetic gastropod assemblage in Lake Malawi. Molecular Ecology 16(3): 517-530.
(Rundom Projects 2.0 LITE)

Gering J.C., DeRennaux K.A. & Crist T.O. 2007. Scale dependence of effective specialization: its analysis and implications for estimates of global insect species richness. Diversity and Distributions 13 (1), 115-125.
(Rundom Projects 2.0 LITE)

Kummerli R. & Laurent K. 2007. Extreme reproductive specialization within ant colonies: some queens produce males whereas others produce workers. Animal Behaviour 74: 1535-1543.
(Rundom Projects 2.0 LITE)

Lehman S.N. 2007. Ecological and phylogenetic correlates to body size in the Indriidae. International Journal of Primatology 28(1): 183-210.
(Rundom Projects 1.1)

Mehner T., Kasprzak P. & Hoelker F. 2007. Exploring ultimate hypotheses to predict diel vertical migrations in coregonid fish. Can. J. Fish. Aquat. Sci. 64: 874-886. (Rundom BC 1.0)

Palma T.P., Poulin E., Silva M.G., San Martin R.B., Munoz C.A. & Diaz A.D. 2007. Antarctic shallow subtidal echinoderms: is the ecological success of broadcasters related to ice disturbance? Polar Biology 30: 343-350.
(Rundom Projects 2.0 LITE)

Simonetti J.A., Grez A.A., Celis-Diez J.L. & Bustamante R.O. 2007. Herbivory and seedling performance in a fragmented temperate forest of Chile. Acta Oecologica 32(3): 312-318.
(Rundom Projects 1.1)

Stewart K., Johnson C. & Godfrey M.H. 2007. The minimum size of leatherbacks at reproductive maturity, with a review of sizes for nesting females from the Indian, Atlantic and Pacific Ocean basins. Herpetological Journal 17: 123–128.
(Rundom Projects 2.0 LITE)

Stroeymeyt N., Brunner E. & Heinze J., 2007. Selfish worker policing controls reproduction in a Temnothorax ant. Behavioral Ecology and Sociobiology 61(9): 1449-1457.
(Rundom Projects 2.0 LITE)

Urra A., Oliva D. & Sepulveda M. 2007. Use of morphometric analysis to differentiate Adelomelon ancilla and Odontocymbiola magellanica (Caenograstropoda: Volutidae) from southern Chile. Zoological Studies 46(3): 253-261.
(Rundom Projects 2.0 LITE)

Williams S.H., Vinyard C.J., Wall C.E. & Hylander W.L. 2007. Masticatory motor patterns in ungulates: a quantitative assessment of jaw-muscle coordination in goats, alpacas and horses. Journal of Experimental Zoology Part A: Ecological Genetics and Physiology 307A(4): 226-240.
(Rundom Projects 2.0 LITE)

2006

Bressler E., Martin R. & Balshine S. 2006. Production and appreciation of humor as sexually selected traits. Evolution and Human Behavior 27(2): 121-130.
(Rundom Projects 1.1)

Ellis A.M, Lounibos L.P. & Holyoak M. 2006. Evaluating the long-term metacommunity dynamics of tree hole mosquitoes. Ecology 87(10): 2582-2590.
(Rundom Projects 2.0 LITE)

Lehman S.M., Rajaonson A. & Day S. 2006. Edge Effects on the Density of Cheirogaleus major. International Journal of Primatology 27(6): 1569-1588.
(Rundom Projects 1.1)

Lehman S.M., Ratsimbazafy J., Rajaonson A. & Day S. 2006. Ecological correlates to lemur community structure in Southeast Madagascar. International Journal of Primatology 27(4): 1023-1040.
(Rundom Projects 1.1)

2005

Chapple D.G. & Keogh J.S. 2005. Complex mating system and dispersal patterns in a social lizard, Egernia whitii. Molecular Ecology 14: 1215-1227.
(Rundom Projects 2.0 LITE)

Goodger J.Q.D., Sharp R.E., Marsh E.L. & Schachtman D.P. 2005. Relationships between xylem sap constituents and leaf conductance of well-watered and water-stressed maize across three xylem sap sampling techniques. Journal of Experimental Botany 56(419): 2389-2400.
(Rundom BC 1.0)

Watson-Capps J.J. & Mann J. 2005. The effects of aquaculture on bottlenose dolphin (Tursiops sp.) ranging in Shark Bay, Western Australia. Biological Conservation 124: 519-526.
(Rundom Projects 1.1)

2004

Castellanos M.C., Wilson P. & Thomson J.D. 2004. 'Anti-bee' and 'pro-bird' changes during the evolution of hummingbird pollination in Penstemon flowers. J. Evol. Biol. 17: 876-885.
(Rundom Projects 1.1)

Hansen I., Brimer L. & Molgaard P. 2004. Herbivore-deterring secondary compounds in heterophyllous woody species of the Mascarene Islands. Perspectives in Plant Ecology 6(3): 187-203.
(Rundom Projects 1.1)

Stiver K.A., Dierkes P., Taborsky M & Balshine S. 2004. Dispersal patterns and status change in a co-operatively breeding cichlid Neolamprologus pulcher: evidence from microsatellite analyses and behavioural observations. Journal of Fish Biology 65: 91-105.
(Rundom Projects 1.1)

Taylor E.B. 2004. An analysis of homogenization and differentiation of Canadian freshwater fish faunas with an emphasis on British Columbia. Can. J. Fish. Aquat. Sci. 61: 68-79.
(Rundom Projects 1.0)

Wenzl T., de la Calle B., Gatermann R., Hoenicke K., Ulberth F. & Anklam E. 2004. Evaluation of the results from an inter-laboratory comparison study of the determination of acrylamide in crispbread and butter cookies. Anal. Bioanal. Chem. 379: 449-457.
(Rundom Projects 2.0 LITE)

2003

Kralik M. & Novotny V. 2003. Epidermal ridge breadth: an indicator of age and sex in paleodermatoglyphics. Variability and Evolution 11: 5-30.
(Rundom Projects 1.1)

Taylor M.I., Morley J.I., Rico C. & Balshine S. 2003. Evidence for genetic monogamy and female-biased dispersal in the biparental mouthbrooding cichlid Eretmodus cyanostictus from Lake Tanganyika. Molecular Ecology 12: 3173-3177.
(Rundom Projects 1.0)

Source: web search results - pdf files. This is by no means a complete list, please report missing articles.