Basically, AVI, MKV, MP4 and FLV are handled very well by FFmpegSource2. The script can be something like this:
LoadCPlugin("ffms2.dll")
FFVideoSource("source.mkv")
Note that I’m using the newer C plugin version.
For M2TS and TS, it seems that by far DGAVCDec is the best choice. Use DGAVCIndex to index the source and you will get a DGA index file. Then write a script like this:
LoadPlugin("DGAVCDecode.dll")
AVCSource("source.dga")