I use ConvertXtoDVD-it can handle most mkv's-you might have to use MKVextract to demux softsubs, though. It can handle h.264-best damn conversion program out there-it gets updated very frequently-output quality is as good or better then CCE (if you set it the highest quality output)-try it-you'll love it!! And ain't nobody slipping me money under the table, either.
I love anime-but I still have a life-but not by choice......?