Just recently finished using Wowza 4 and the Transcoder in anger. The transcoder really is so efficient and great quality... I just wish Wowza would make a stand-alone version for transcoding videos for VOD :-)
File transcoding for vod is a possible future feature of Wowza, but I don't have a time frame for that. Meanwhile you can use
Encoding.com with Wowza. And we are working on adding
Encoding.com integration in the Wowza Module Collection, but that is not in place at present.