According to the YouTube official blog post. All new videos uploaded to YouTube are now transcoded into WebM. To put that in perspective, nearly 6 years of video is uploaded to YouTube every day. So far they have already transcoded videos that make up 99% of views on their site or nearly 30% of all videos into WebM.
From the offical blog post:
To that end, all new videos uploaded to YouTube are now transcoded into WebM. WebM is an open media file format for video and audio on the web. Its openness allows anyone to improve the format and its integrations, resulting in a better experience for you in the long-term. As we work to transcode more videos into WebM, we hope to reduce the technical incompatibilities that prevent you from accessing video while improving the overall online video landscape.
YouTube will continue to support the H.264 codec and Adobe Flash player, but they are committed to developing their own HTML5 video player.