i need some software that can encode mpeg2/dvd sorta files into .mkv h264/lame .. but i also need it to have filters like deinterlace/crop/resize n stuff like that.. is avisynth + megui + mkvtoolnix what im lookin for?
If you want to encode using H.264, have a look at Handbrake or FairUse Wizard. Also Avidemux probably has the features you want.