Ah, you are probably right about the playback. I have both installed - if you say it's XiphQT that enables Safari to use Theora, you're probably right.
As for the encoding, I was using ffmpeg2theora 0.25, which according to the release notes bundles libtheora 1.1. Whether or not I'm using it optimally, though, I can't say. I was loosely following the instructions for batch encoding here:
I was actually hopeful that Perian had started supporting it, I'd guess their installed base would be much higher than XiphQT which would mean, e.g., Wikipedia content just working for many Safari users.
But I checked the site, they only do vorbis in mkv.
As for the encoding, I was using ffmpeg2theora 0.25, which according to the release notes bundles libtheora 1.1. Whether or not I'm using it optimally, though, I can't say. I was loosely following the instructions for batch encoding here:
http://diveintohtml5.org/video.html
.. but no matter what I do, the .ogv comes out looking like a poorly encoded DivX.
Anyway I'll keep trying, thanks for the correction on the QT plugin.