Yeah, I'm aware of that document. Just proves that DI never had any real science on their agenda - it's all about defending their mythological agenda.
Direct Experimental Tests Of Evolutionary Concepts
Cavefish as a Model System in Evolutionary Developmental Biology by William R. Jeffrey, Developmental Biology, 231:, 1-12 (1 Mar 2001) - contains experimental tests of hypotheses about eye evolution
Crystal Structure Of An Ancient Protein: Evolution By Conformational Epistasis by Eric A. Ortlund, Jamie T. Bridgham, Matthew R. Redinbo and Joseph W. Thornton, Science, 317: 1544-1548 (14 September 2007) - refers to the reconstruction of ancient proteins from extinct animals by back-tracking along the molecular phylogenetic trees and demonstrating that the proteins in question WORK
Evidence for rapid speciation following a founder event in the laboratory by J.R. Weinberg V. R. Starczak and P. Jora, Evolution vol 46, pp 1214-1220, 1992 - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY
Experimentally Created Incipient Species of Drosophila by Theodosius Dobzhansky & Olga Pavlovsky, Nature 230, pp 289 - 292 (02 April 1971) - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY
Founder-flush speciation in Drosophila pseudoobscura: a large scale experiment by A. Galiana, A. Moya and F. J. Alaya, Evolution vol 47, pp 432-444, 1993 - EXPERIMENTAL GENERATION OF A SPECIATION EVENT IN THE LABORATORY
Genetics of Natural Populations XII. Experimental Reproduction of Some of the Changes Caused by Natural Selection by Sewall Wright & Theodosius Dobzkansky, Genetics, 31(2): 125-156 (1946) - direct experimental tests of natural selection mechanisms
Hedgehog Signalling Controls Eye Degeneration in Blind Cavefish by Yoshiyuki Yamamoto, David W. Stock and William R. Jeffery, Nature, 431: 844-847 (14 Oct 2004) - direct experimental test of theories about eye evolution and the elucidation of the controlling genes involved
Initial Sequenceing of the Chimpanzee Genome and Comparison with the Human Genome, The Chimpanzee Genome Sequencing Consortium (see paper for full list of 68 authors), Nature, Vol 437, pp 69-87, 1 September 2005 - direct sequencing of the chimpanzee genome and direct comparison of this genome with the previously sequenced human genome, whereby the scientists discovered that fully twenty-nine percent of the orthologous proteins of humans and chmpanzees are IDENTICAL
Origin of the Superflock of Cichlid Fishes from Lake Victoria, East Africa by Erik Verheyen, Walter Salzburger, Jos Snoeks and Axel Meyer, Science, vol 300, pp 325-329, 11 April 2003 - direct experimental determination of the molecular phylogeny of the Lake Victoria Superflock, including IDENTIFYING THE COMMON ANCESTOR OF THE 350+ SPECIES IN QUESTION and NAMING THAT ANCESTOR as Haplochromis gracilior
Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity by M.E. Boraas, D.B. Seale and J.E. Boxhorn, Evolutionary Ecology Vol. 12, no. 2, pp. 153-164. Feb 1998 - direct experimental test of hypotheses about the origins of multicellularity
Resurrecting Ancient Genes: Experimental Analysis Of Extinct Molecules by Joseph W. Thornton, Nature Reviews: Genetics, 5: 366-375 (5 May 2004) - direct experimental reconstruction in the laboratory of ancient proteins from extinct animals
Sexual isolation caused by selection for positive and negative phototaxis and geotaxis in Drosophila pseudoobscura by E. del Solar, Proceedings of the National Academy of Sciences of the USA, vol 56, pp 484-487, 1966 - direct experimental test of selection mechanisms and their implications for speciation
The Master Control Gene For Morphogenesis And Evolution Of The Eye by Walter J. Gehrig, Genes to Cells, 1: 11-15, 1996 - direct experimental test of hypotheses concerning eye evolution including the elucidation of the connection between the Pax6 gene and eye morphogenesis, and the experimental manipulation of that gene to control eye development
The Past As The Key To The Present: Resurrection Of Ancient Proteins From Eosinophils by Steven A. Benner, Proc. Natl. Acad. Sci. USA., 99(8): 4760-4761 (16 April 2002) - direct experimental reconstruction of ancient proteins from extinct animals
This list is by no means complete, because over eighteen thousand critically robust peer reviewed papers were published in evolutionary biology in 2007 alone. The number of papers published in the subject since Darwin first published The Origin of Species probably exceeds a million or so, if someone were ever to perform the requisite accounting.