Interesting. If one looks at your list, which clearly is less "biased" towards academia, it seems like it might indicate more accurately those organizations that produce research that is actually "useful"/influential, no?
More likely it looks like bias favoring cross-disciplinary research. Different fields have different typical citations rates. Biological sciences tend to have orders of magnitude higher impact factors than other fields [1].
So, for example, if you CS paper touches some bio topic, it will gather a lot more citations, also it will have much higher chance to appear in high impact factor general science publications like Nature/Science.
For the companies, there can be bias from higher availability of freely accessible full-text articles. I remember there was some analysis in Nature of how online availability increases citations [2]. Companies are more likely to put their papers online and also have better "SEO", so more people are going to see and cite their papers.
It varies by company and era, but companies also pull a lot of citations that aren't really to the research content of the paper so much as to the mere fact that the paper exists, documenting that X was used by Company Y. (Academics also get a bunch of those kinds of throwaway citations, but I think it's considerably higher for citations to industry papers.) It's often useful if you're working in a theoretical area especially to be able to throw in a few cites of the "hey people really use this!" variety--- "similar ideas are used in deployed systems by Microsoft [1] and Google [2]" type things.
For example, if you were to look through the absolutely colossal number of citations that Google's MapReduce paper has gotten, the vast majority are supporting statements like "parallelism is important" or "these kinds of techniques are used in practice" or "a common current approach is". Not that it doesn't have a bunch of citations actually about the paper as well, but I'd suspect that it has more of these "free" kinds of citations than most papers do.
UPR8011 Centre d'Elaboration des Matériaux et d'Etudes Structurales 187.36
J. Craig Venter Institute 70.09
Sri Lanka Press Institute 56.33
European Molecular Biology Laboratory 43.45
Apple Computer, Inc. 41.84
Wellcome Trust Sanger Institute 36.47
Swiss Institute of Bioinformatics 32.86
Google Inc. 28.5
European Bioinformatics Institute EMBL 28.2
Digital Equipment Corp. (DEC) 28.12
Palo Alto Research Center 27.21
Howard Hughes Medical Institute 26.18
Sun Microsystems Laboratories 24.43
Harvard University Harvard Business School 24.35
AT&T Labs Research 23.04
Santa Fe Institute 21.65
National Institute of Genetics Mishima 21.24
Salk Institute for Biological Studies 20.67
Bell Labs (Lucent Technologies Inc.) 20.53
University of California Berkeley 20.53
Weizmann Institute of Science 20.52
Yahoo Research Labs 20.28
University of London 19.69
Stanford University 19.63
Princeton University 19.51
Massachusetts Institute of Technology 19.14
Cisco Systems, Inc 19.06
Argonne National Laboratory 18.81
Microsoft 18.69
National Institutes of Health 18.34