While on that note, what’s the best tagging software to use? Foobar tags don’t always agree with iTunes or vice versa.
For both Unicode (preferrably UTF-8 flavour) is the modern way to go.
For MP3s I use ID3v2.4 tags with UTF-8 encoding and explicitly disable the generation of ID3v1. v1 is deprecated and its functionality is too limited for modern use.
For everything else I use the native tagging format, like Vorbis comment for Ogg Vorbis and FLAC. Vorbis comment internally encodes all strings in UTF-8, so no problem here with any kind of language.
Concerning filename encoding and transfer between different operating systems. Well, you need a software that honors the encoding when compressing the files (and a archive format that can store the encoding) and of course your destination system has to do the same. ZIP is deprecated since it became a huge hack over the years. Both RAR and 7zip can store UTF-8 encodings (and probably a lot more) and therefore retain file encoding.
Here some Wikipedia articles, that could be interesting for you:
http://en.wikipedia.org/wiki/ID3
http://en.wikipedia.org/wiki/Vorbis_comment
http://en.wikipedia.org/wiki/Unicode
http://en.wikipedia.org/wiki/UTF-8
http://en.wikipedia.org/wiki/RAR
http://en.wikipedia.org/wiki/7z