The issue you're going to have is two-fold.
The X10's EXR sensor is not something other cameras have, save for a couple of Fuji cameras. The EXR sensor can do a lot of things with the available pixels in the sensor and that is why their RAW files are a little odd compared to those of say the X-Pro1 or 100 which use the X-Trans sensors.
You'll potentially have a RAW image that contains the pairs of pixels, and a lot of RAW software doesn't expect there to be a 12mp sensor with a 6mp image, twice. When you're using the EXR modes on the dial you cannot also capture RAW, but you can force the camera to use the EXR sensor in this way by setting the size of your image from Large to Medium and then use RAW+JPEG.
In-camera RAW conversion to JPEG will do the binning of those pixels properly and always get great results (though believe me, I can understand not wanting to sit around with your camera in your lap for an hour doing trial and error conversions on a 2" LCD.)
Fuji doesn't publish the format on these to my knowledge, which is why there isn't native support for the X10's RAW in Aperture. Adobe Lightroom will convert it to Adobe DNG, or you can use the Adobe DNG converter, which may or may not help you (I don't know if there is a DNG converter for computers running FOSS).
Ultimately if FOSS compatibility and capability for RAW is really important to you, the X10 isn't going to make it easy for you (or even mildly annoying); there are better purchases within those constraints. The quirks of the X10 (or any other camera) take some practice and experience; I'm not delighted with the way I'm handling the X10's RAF RAW on OS X and Aperture, but at least I have the benefit of being able to make do with DNG converter. I knew that I'd have some rough ground to cover before I purchased it, but after using the X-Pro1 for a while (and having it outside of my budget) I couldn't see myself liking anything else more.
Update: I have used dcraw and ufraw-batch and made TIF and PNG images, they were pretty good. The JEPGs out of the camera are arguably better though, which is further evidence that the RAW-to-X software out there (other than the bundled SilkyPix) may not always handle the binned data correctly. Or I'm really bad at processing images (very likely!) and can't match the camera because I'm a dunce!
IMO, Fuji's quality control is outstanding, the X series are built in Japan and use excellent components. The 'White Orbs Problem' has never affected more than 1 out of 10,000 photos I've taken and if I sent in a camera for repair and it came back with dust in the lens I'd just send it back. It isn't like Fuji engineers are doing the labor on that.