For reading and manipulating raw files I am using
ufraw which is based on dcraw. To read the X100's files I convert them to DNG with Adobe's DNG converter.
In the color management section it is possible to select a camera profile, e.g. color matrix, AdobeRGB1998 and to set the gamma correction and linearity.
Output and input profiles can also be selected. Color management is based on
LittleCMS, a small footprint color management engine.
If I am using a camera profile for the NikonD90 the colors match quite closely to what I see in lightroom or silkypix, but the reds are a little bit off, they tend a bit more to orange. I think it should be possible to fix that with a specific profile for the X100, but I have not found out how to get one or how to modify an existing one.
I am using ufraw because it is pretty, pretty fast and straight forward. It works very well for black and white and should work also quite decently for color, given that one has a correct profile for the camera. I guess in a next release the X100 will be supported, as ufraw is based on
dcraw, which already supports the X100. Did I mention that ufraw is fast?