About a month ago,
Bob posted an entry about how to convert video for the iPhone/iPod touch. I read it with interest because I was having issues encoding soft-subbed anime commonly found in the mkv format. To my disappointment though, these kind of files gave Bob some trouble as well and I personally wasn't interested in paying for Quicktime Pro.
Other applications I've found for encoding were either bloated, confusing, or full of ads. They also did not handle mkv well and, for some, setting up batch encodes was a chore.
As a result, I decided to make my own conversion tool based on the same encoding process we use on the org for streaming video. I don't know how to write desktop applications so unfortunately I was stuck with MS-DOS batch files. However, I'm happy to say that after some help from Scott and some feedback from some a-m-v.org users, I have a working converter that will batch process just about any video file you throw at it, including soft-subbed anime.
After you've set up the encoder, the process is very simple. You simply copy or move the files you want to convert to a folder and execute the batch file. When the process is complete the files that were in the folder will have been converted. The original files will be moved to another folder as they are done encoding. The encoded files should play back on any device that can support the H.264 baseline profile. (iPhone, Android phones, PS3, etc.)
If this sounds useful to you then you can find everything you need to know here:
http://www.animemusicvideos.org/forum/viewtopic.php?f=46&t=95586