I'll test the next software:

Adobe DNG Converter ver.

DNG Converter is distributed by Adobe for free to convert a proprietary raw formats to open standart of format for raw files called DNG (digital negative). It's not suited to process final jpeg images, but it makes demosaicing too to create jpeg preview embedded into DNG files. That can be extracted later for test purpose (I used "dcraw -e *.dng"). Also I want to test how it's good in conversion of such non-standard X-Trans raw files to DNG. 

Adobe Photoshop Lightroom ver. 4.3

Perhaps Lightroom is the most popular raw convertor. But it's support of X-Trans raws is far from ideal, that's why I began this tests.

Raw File Converter EX powered by Silkypix ver.

This Raw File Converter EX is an official Fujifilm converter distributed for free. Looked like old version of Silkypix Developer Studio with support of new Fujifilm cameras.

Silkypix Developer Studio Pro ver.

This is the latests commercial variant with new algorithms for colour processing, so looked different. I downloaded Silkypix DSP 5 trial from the Silkypix site.

Capture One Pro ver. 7.0.2

Capture One Pro is well known raw converter, I downloaded trial to test.

DxO Optics Pro ver. 8.1.2

I like how DxO lab tests cameras and lenses, so I downloaded latest trial of DxO Optics Pro 8. But this program does not support X-E1. You can see RAF files in the file browser of DxO, but all of them marked as "uneditable". Okey, I thought, let's test linear DNG on it. But... It doesn't show in file browser any converted DNG (by Adobe converter) at all with any compatibility settings. But it fine works with DNG created by Pentax K-5 camera (DNG become Pentax standard for raws). That's why it wasn't tested.

ACDSee Pro ver. 6.1

ACDSee Pro is a known name and has a trial. But ACDSee does not recognize X-E1 RAF files.

Dcraw ver. 9.17

Dcraw is a very small free open-source program written in ANSI C and thus can be compiled on almost any operational system. It has simple interface of "command prompt" and thus is not convenient for a common user. But there is a lot of GUI program (open source and commercial) based on it and due to this it's interesting to test this software. Dcraw was compiled and tested under Debian Linux. I used "dcraw -w -W" for image with camera settings and "dcraw -a" for autocorrection.

Raw Therapee ver.

Raw Therapee is a well-known open-source free program based on tweaked Dcraw. It exists for Windows, MacOs and Linux. I downloaded version for Windows 64-bit. But it crashes when I tried to open X-E1 RAF files.

I didn't test Aperture and Raw Photo Processor because I have not MacOS.