GIMP opened the raw files up from my S3IS with no problem. The latest version of gimp includes ufraw as a plug. When the file is opened in gimp, the ufraw dialog window opens. Ufraw has the camera profile, so it was easy to adjust the white balance. I had to select tungsten in ufraw window for my test, because it was an indoor shot. QTPFSGUI also opens the files directly, which I am using to make HDRs. Both of these are open source.
To make the HDR correctly the white balance has to be corrected first. I tried doing the HDR and then the white balance, and some colors (in my case blue) got blown out. I did the white balance in ufraw/gimp, saved as an uncompressed tiff, and then made the HDR in qtpfsgui and IMHO it resulted in a significantly sharper final photo than using the jpeg off the camera.