What's the best solution to convert
.mkv files to
Try Any Video Coverter (Free Software)
Also you can download and add codec for extra format like WMA and RealVideo.
if you want to see this Videos on your Apple Mobile Devices (iPod Touch, iPhone or iPad) I would strongly suggest that you get your hands on Air Video
Then, download and install in your Windows or Mac the free server application and tell it to "see" all folders you have videos on.
you can now access from your mobile devices, all Videos ad if you have a good Dual Core 2 (or up) CPU in the machine you installed the "Server", you can see all videos with their "Live Conversion", in other words, you can see them 5 seconds after you tap PLAY, instead waiting for the conversion is ready.
pressing the Add to iTunes, it will convert and add to your iTunes list directly (if you want to see "offline" / not in the same WiFi as your server)
give it a try!
P.S. if you only wish to convert videos and add them into your iTunes list, just use the free Server Application, no need to have the AirVideo App, this is only required if you want to watch the videos on your devices.
My go-to application for all video conversion. I would highly recommend MPEG Streamclip. It should be able to handle what you want to do. And...it's free!