Hola Illumin,
Now that I am understanding the intricacies of video file formats more and more, I am beginning to really use EM Total video converter as my default converter.
I am writing this also as a piece of info for the general public so forgive me if Im going over anything you already know.
TVC has 2 things going for it that make it my converter of choice in regards to anime
1) It has a built-in setup for hard encoding subtitles into a video. You can select FILTERS in the file window where you can actually setup subtitles , watermark etc. I used to run files under Virtual Dub to do this.
2) Under TOOLS on the bottom right corner there is a demuxer and multiplexer. This is hugely important since it allows me to work with files such as some MKV and any OGM I couldn't touch before. Once I understood these file formats are made up of component pieces of video, audio and subtitles, it becomes a simple matter of breaking files up (demux) then rejoin (multiplex) them into formats I can use.
For example, Ultral MKV was producing junk when I put some MKV files through it. When I broke open these files using a demuxer, I discovered that the audio they use is OGG format. Ultra MKV cant handle it. So I changed the audio to MP3 and then multiplex back the video and convert that with the subtitles in them.
Granted this may sound like a lot, but with the right programs its actually not bad.
1) Demux MKV or OGM file (separate programs MKVextract or OGMdemuxer)
2) If the audio is the issue, which is often the case, I use Audacity (another complete separate program) to convert the audio track I want to MP3
3) Multiplex back with Total Video Converter tools.
4) Convert the new joined file with the subtitles with TVC
Figuring it all out took a while, but with this process I can convert a 30 min episode to my Nokia N800 or IPod touch in about 18 min. processing time.
At the end of the day, a lot converters pretty much call on FFDShow or Memcoder or some other commonly available tool which is often free. What makes it worthwhile for the end user becomes a matter of ease of use and feature set (ie what files can it convert, can it add subtitles, etc..)