IBM:

    Without the benefit of patent protection, software companies
    would be forced to rely on secrecy which limits the public’s
    ability to learn from software innovations, since patent
    documents are a significant source of technological disclosure.
    See, e.g., In re Alappat, 33 F.3d 1526, 1571 (Fed. Cir. 1994)
    (Newman, J., concurring). Given the reality that software source
    code is human readable, and object code can be reverse
    engineered, it is difficult for software developers to resort to
    secrecy. Thus, without patent protection, the incentives to
    innovate in the field of software are significantly reduced.
    Patent protection has promoted the free sharing of source code
    on a patentee’s terms—which has fueled the explosive growth
    of open source software development.

and

    The economic benefits that flow from software innovation are the
    product of significant investment in research and development.
    And the incentives provided by the patent system encourage that
    investment by providing the same quid pro quo as in other
    technology fields: the promise of economic rewards in exchange
    for the public disclosure of useful inventions. See generally
    Testimony of Nicholas M. Donofrio, Executive Vice President,
    Innovation and Technology, IBM Corp., Before the H.R. Comm. on
    Science (July 21, 2005); Cong. Office of Tech. Assessment,
    Finding a Balance: Computer Software, Intellectual Property, and
    the Challenge of Technological Change, 23 (1992) (recognizing
    that “patent protection is of importance to the U.S. software
    industry”). The exclusive rights granted to patentees
    encourage software innovators to pursue inventions that they
    might not otherwise pursue, in broad and diverse areas.

and

    Patent protection for software protects innovators from
    appropriation of their efforts by “free-riders.” Without
    patent protection, the risk of appropriation may force software
    innovators into other, more promising ventures. See, e.g.,
    Richard S. Gruner, Better Living Through Software: Promoting
    Information Processing Advances Through Patent Incentives, 74
    St. John’s L. Rev. 977, 1004 (2000). The free-rider problem is
    particularly acute in the software sector because software
    products are “vulnerable to rapid, inexpensive copying that
    undercuts the initial developer’s opportunity to benefit * *
    *, thereby undermining its incentives to invest in software
    development.” Pamela Samuelson, et al., A Manifesto Concerning
    the Legal Protections of Computer Programs, 94 Colum. L. Rev.
    2308, 2332 (1994). While literal copying is the province of
    copyright law, the ease of appropriating software source code
    makes the patented inventions included in the code uniquely
    susceptible to instant appropriation.

These are all taken from the amicus brief IBM filed in the Bilski case. http://www.patentlyo.com/08-964-ibm.pdf

edit: fixed to replace duplicate quote with the quote I meant to paste in.