Gordian Knot is a very good tool for the Pro's especially because it automates some of the more simple but timeconsuming things like AR and bitrate calculation, but still gives you the chance to fiddle with very complex avisynth scripts for filtering and blending/deinterlacing.
There are 2 other tools that i can recommend to the more 'basic' users, namely DVX and DVDtoOGM ( soon DVDtoMKV ).
DVX requires the .NET framework to be installed on your PC, what is scaring off many users because they dont trust Redmond. However, i have it installed on my Win2k box and its working fine for me, and DVX even has very good matroska support already, including anamorphic encoding wihtout resizing filter ( it looks marvellous for 2 CD rips, try it ! ), only disadvantage is you have to set the AR in the MKV header manually using the shell extension or the TCMP CDL.
As for DVDtoOGM, this tool will go opensource and become the new 'official' matroska creation tool then, renamed to 'DVDtoMKV' . The muxing process will be done with mkvmerge and it will allow
- direct vobsub muxing, compressed and uncompressed ( no OCR necessary )
- AAC an HE-AAC muxing
- SSA subs muxing
- anamorphic encoding with automatic AR setting in the track header ( mkvmerge )
- tagging
etc.
A more detailled spec can be found on corecodec.com in the forums
About FlaskMPEG : i wont use it as long as there is no MKV support for it

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