There are several free software packages available at:
http://www.rwjms.umdnj.edu/research/cdf/experimental/analysis.html They have CDPro, CONTIN, CCA, DICHROPROT, K2D, SOMCD and several others.
K2d software can be accessed at: http://www.embl-heidelberg.de/~andrade/k2d.html or http://kal-el.ugr.es/k2d/k2d.html You can send your data to a web server or get the program for yourself.
There is also an online facility for analyzing CD data called DichroWeb in England at: http://dichroweb.cryst.bbk.ac.uk/html/home.shtml They support the programs CONTINLL, SELCON3, CDSSTR, VARSLC and K2D. You must register for an account with them and always reference them if you use their services.
For a comparison of some of the above programs, see Sreerama, N. and Woody, R. W. (2000) Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set Analytical Biochemistry, 287, 252-260.