If all you want to do is convert an ogm file to mkv, or change the order of streams so that Japanese audio is first, there generally isn't any need to re-encode the whole video, assuming the video itself is h.264 to begin with. That takes hours, will have a quality impact, and is often unnecessary. You might need to re-encode it if you want to change the h.264 profile, and you definitely will if you want to change things like the bitrate etc. But other than that, you can just demux all the streams contained in the ogm file, then mux them into an mkv file instead.
Well, converting ogm to mkv is just the immediate task. Maybe I was not clear enough, but, in the long-term, these are the tasks which would require the use of a converting tool (for which I opened this inquiry), depending on files in question:
1. Converting old containers like ogm into newer ones, like mkv.
2. Converting h.264 profiles from Level 5.1/5.0 to 4.1 (primary)
3. Changing the default audio stream and subtitle (where it is the case) so that japanese audio + english subtitles would be default.
4. Changing the audio codecs to AAC/AC3 (where it is the case).
Those are all I can think of right now. Things like bitrate, framerate, sampling rate, resolution will stay as they are in the original files.
As you probably noticed, it is basically a compatibilization of video files with blu-ray standards. As you might now, some of the fansubbing groups have rushed to use the most advanced h.264 Profiles like 5.0 or 5.1. From having watched both on my PC, I fail to see what benefits do 5.0 or 5.1 provide particularly for resolutions of 1280x720 or less in order to sacrifice for it the compatibility with an entire class of media hardware. The same can be said about the High 10 profile, which had been lauded as "providing better image" or "less size" or whatever, but it does neither, quite the opposite, it makes the picture look like crap. The first time I saw a video file encoded in High 10, my reaction was "what the hell is this shit", because the color of the image looked from place to place like a painting over which someone spilled some drops of water.
Anyway, to each their own, but, as far as I'm concerned, I would rather get rid of all these needless "bells and whistles" with which some groups adorn their releases for no gain which I can see, as I much rather prefer to watch the videos from a blu-ray player than a PC and it does not really cost me anything to re-encode them. The amount of time required would have been indeed a concern in the past, but, with the power of the most recent CPUs, is not one anymore. For instance, my CPU is a Intel i5200K Sandybridge at 3.3 Ghz which takes less than 8 minutes to encode a 300 MB files. Basically, if I leave it on a task over night, it can do an entires series of 60-70 episodes until the morning. Which is a satisfying speed, especially having in mind that not all the series would need re-encoding, but just a part of them.
For this task, I had one tool, MediaCoder. While it has all the features one could desire, it has one major drawback: you are constantly pestered with requests for donations. As such, I decided to test the waters which are the best tools used for encoding/re-encoding and, from all the suggestions, pick the one which suits my needs the best.
Handbrake is an acceptable option. It has less features than I would like, but it's usable.
X-Media Recode seems to be a very good choice as well. So, everything is fine for all aspects, except one: I can't figure out what happens with the subtitles tracks when converting from ogm to mkv. Both handbrake and X-Media Recode have the option to select which subtitle track you want to include in the output file, but no text appears (and, yes, I know where you select the subtitle track - in the WMP which I use, it's in the navigate/subtitle language, but the text simply dissapears during the conversion).
It's not necessarly something crucial, as ogm files which I need to convert are very few - is an antique container which was abandoned a long time and, for the few files still left encoded in ogm, I can dispense with them. But I would like to know what is the problem, if possible.