I guess the biggest change in 0.99.06.041 is that the documentation has been brought up to date, including the screenshots. I strongly recommend re-reading the documentation or at least reviewing the annotated screenshots.
Better ReplayGain support, so an additional format is now recognized.
I fixed several bugs that could cause crashes.
The export functionality allows a locale to be specified when saving to .m3u; the XML format now works OK when names contain double quotes.
Several versions ago the option to compile the project with Visual Studio was added. Although the program started OK, it could crash or do unexpected things when trying to apply transformations or save from the tag editor. This is fixed now.