If you use CFit, you can refer to the following publication :
Gay, L., P. Crochet, D. Bell, and T. Lenormand. 2008.
Comparing genetic and phenotypic clines in hybrid zones: a window on tension zone models.
Evolution 62: 2789-2806

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CFIT-6

If you have only genetic data, CFit-6 is the easiest user-friendly version.

You can download it here
Simply dezip in a folder and click on the cfit.exe to run.
An example for the input file is included in the zipped file.
You can find more information by using the 'help' button in CFit.

Another version of CFit6 can be used for 2-Dimensions data.
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CFIT-7 (Dec 09 version)

If you have genetic and/or phenotypic data, CFit-7 is the version to use.

You can download it here
Simply dezip the package in a folder and click on the cfit.exe to run.
An example for the input file is included in the zipped package.
An example of mathematica file using CFit7 output is also included in the zipped package.
This mathematica file shows how to produce figures such as the one displayed below.
You can find more information by using the 'help' button in CFit.

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CFIT-7 2D scaled (Dec 13 version)

Here is a version of CFit that incorporates 2D spatial data as well as scaled logit shapes
(i.e. semi diagnostic markers). It also contains a subversion allowing to fit dispersal from the
rate of decay of neutral clines through time. This method is implemented in Rieux et al (2013). 
The PDF of that paper is included in the zipped distribution package along with help files.
Refering to this publication would be apreciated if you use the method.

You can download it here

Simply dezip the package in a folder and click on the .exe to run.
An example for the input file is included in the zipped package.
An example of R file using CFit7 output is also included in the zipped package.