I want to be able to playback my BDs with no quality loss, and with as little overhead as possible. m2ts contains a lot of overhead; demuxing to mkv will save a few gigs right there, and then of course there is the big space saving you get by converting lossless tracks to flac, so for me I only us eac3to. Then of course, I don't at all like using PDVD or TMT, while I have a fond place in my heart for MPCHC, so mkv's via eac3to is perfect there as well.
@fido, every once in a while you'll come across a movie where, even though there is no seamless branching, the beginning or end or whatever of the movie will be in a different m2ts file. eac3to is great, because if you just point it to the main directory containing the files for a BD you've ripped to your HD, it will tell you which playlist contains all the files necessary for getting a complete version of your movie. From there you just select the playlist, and eac3to will combine everything into one file, correcting any audio gaps that might exist. You might be able to do this with tsmuxer, but I've never even used that software, because eac3to is perfect for what my requirements are.