Changing the input and output encodings in GeoMOOSE is done via the local settings.
In the conf directory open the local_settings.ini file and add the following lines to change GeoMOOSE to UTF8:
[encodings]
input-encoding=UTF-8
output-encoding=UTF-8
This has been only really tested with UTF-8 and Latin1 encodings. None of the core team speaks a non-Romanitic-influenced language.