Sometimes converting to other formats is beneficial. Take Nero Vision (9)for instance. It doesn't like MKV files. But MKV2VOB can output to AVCHD/M2TS without encoding(use it for inserting Black bars). Apparently the program need only change a few bits of data
OGG audio or FLAC isn't very common. But MP3 and Wav are
Perhaps this is a bad example though. I certainly have no current need to convert DTS to WAV.