VLC is more of a media player then an editing tool, I believe.
Well, I use virtualdubmod for pretty much everything but batch transcoding. Problem is .wmv files don't work because of a "microsoft copyright violation" so I use a program called "winavi" for converting those.
And for making dvds I use either "NeroVision Express" or "Convert X to DVD".
.mkv I avoid like the plague though, it seems like only anime fansub groups use it, and only because they know its hard to make a DVD out of, thus stopping fansub sales on Ebay.