LoopAuditioneer is a software I've written that can do a lot of things to ease sample production. Loops, Cues, Pitch info and a few other things can all easily be done with it. It's free GNU/GPL software. The link will take you to my sourceforge page where you can find both the source and binaries.
NoisePipes is another software I've written that's fairly specialized. It's intended for effect stops that have an attack sample and a separate release sample but no loops in the attack. The software generates ODF lines to be able to use such samples in GrandOrgue. It's free GNU/GPL software and the link above takes you to to the source folder of NoisePipes that resides in a collection repository called grandorgue-odf on GitHub. Compiled binary file for Linux here (you need to have wxWidgets and libsndfile packages installed too), and for Windows here.
jMakeOdf (last updated 2016-02-04) is based on (partly ported from) make_odf by Jean-Luc Derouineau. The software is written by me in Java to be easily used on different operating systems and can help with the most heavy workload of creating organ definition files (ODF) for GrandOrgue. As such, the resulting files will need some manual adaptation but the most repetitive tasks has been automated. The software is free and released under a MIT license. The package that you can download from the link contains both instructions, the jMakeOdf.jar file and the sources. The source files can also be found in this subfolder of grandorgue-odf on GitHub where you also can find more example shorthand definition files.
jOdfCleaner (last updated 2014-07-17) is a simple commandline based program that will try to clean .organ files made for older versions so that they can be used with recend GrandOrgue versions without so many log warnings. The software is free and released under a MIT license. The package you download from the link above contain instructions, the jOdfCleaner.jar file and the source code. The source code is also part of the grandorgue-odf repository/project on GitHub.
The GitHub repository grandorgue-odf contains different tools that help with ODF creation for GrandOrgue. Maybe you can find something that suits your needs there.
Nick Appletons NoiseReduce is a software that works wonders with otherwise impossible samples. All my samples are processed with it and I think it's not to much to say that without this software the scene of free samplesets for GrandOrgue would look quite different indeed! The link takes you to Nicks webpages for NoiseReduce.
Last but not least, don't forget to often visit the GrandOrgue Sourceforge page to look for updates of GrandOrgue. The development is highly active and you can find lot's of interesting things as well as possibilities to participate in this project there. This software is a source and reason for much creativity in different ways, support it by getting involved!