I just switched to Mutagen as the metadata handler for my mkogg utility. I used to use metaflac and id3v2, but ran up against limitations discussed on the mkogg page. Here's a quick note on using Mutagen to set some ID3 tags:

>>> from mutagen.mp3 import MP3
>>> import mutagen.id3
>>> audio = MP3('some_file.mp3')
>>> audio['TIT2'] = TIT2(encoding=3, text=["Title"])
>>> audio.save(v1=2)  # also include ID3v1 tags, when possible

ID3v2 encodings are hardcoded to the following table:

0ISO-8859-1 (ASCII)
1UCS-2 in ID3v2.2 and ID3v2.3, UTF-16 encoded Unicode with BOM.
2UTF-16BE encoded Unicode without BOM in ID3v2.4 only.
3UTF-8 encoded Unicode in ID3v2.4 only.

In order to get ID3v1 tags, you'll need to use frames and encodings that ID3v1 understands. For encodings, that means 0 (ISO-8859-1).