As of Mac OS X 10.6 (Snow Leopard) the way OS X decides what application opens which files has changed. Many people complained about this, just google for UTI (Uniform Type Identifier) and Snow Leopard, you'll see Gruber and Dilger have their say about it.
Fact is: QuickTime does not open .mkv files anymore, it's not in its list of UTIs it handles. For those who relied upon Perian for playing Matroska video files poses a problem. A work-around is installing NicePlayer which tells QuickTime to add .mkv files to its list, this means installing a new QuickTime front-end, or you can run this little application that I've compiled from Perian's Subversion repository (build 1168) which is basically what Perian's installer will run when they finally decide to release a new version. Just like NicePlayer it will tell QuickTime about some extra movie types.
With the release of Perian 1.2 it tells QuickTime about .mkv files in the way I described. I removed the download link.