Tools

I mostly use ufraw as my raw converter.

Important for good results is that the correct color profile for the camera is used. This can be set in the 'color management' tab. The tricky part is aquiring the camera profile.
There are some open profiles for different cameras available at the ufraw homepage.

Another way to aquire a profile for your camera is (at least for Canon) the following way. Install the Canon software under windows (does not work with wine). Search the install directory for .icc files. Copy those to somewhere you can access them from ufraw.

Geeqie is a fork of gqview. I.e. it is an imageviewer which is raw-aware. Geeqie displays jpg and corresponding raw files as the same file for easy browsing, but allows editing of each file individually. Its fast, easy to use, but provides a lot of functionality for the photo editing workflow. E.g. you can launch a raw image directly in ufraw or any other (configurable) tool.

Hugin is a photo stitcher. If you compile hugin yourself, make sure you enable sift support. Sift automatically searches for matching points in two images. Doing that by hand is quite the pain.

Rawstudio is another raw converter.

Gimp The GNU Image Manipulation Program.

Digicam is for photo management. The big advantage of digikam, in my opinion, is that image collections in the program are reflected in the folder structure on disk. Photos can therefore be sorted in digikam, but you can browser them with any other programs.