I haven’t tried this one out yet, but another product from Pegasys is already my favourite video encoding tool. I use TMPGENc Xpress 4.0 for most of my high quality video encoding already.
VideoSync from the same guys seems like a promising product. It supports DVR-MS files from Windows Media Center Edition (in addition to a bunch of other formats).
The most interesting feature is the possibility to set up a watch folder. Meaning that you can tell the software to constantly watch a folder on your computer and immediately start transcoding and publishing to your favourite mobile device if a new file arrives in this folder.