Thanks! I've added a section about joining MKV files as well now (for films such as the extended edition of Avatar / LOTR that span 2 disks.)
Hopefully it'll be of use to a few people - all the other guides I've found thus far tend to miss out relatively important steps (such as forced subtitles), rely on paid software or demos rather than free / open source stuff, or use really old outdated codecs like xvid / avi that give you horrible compression rates for your file size.