HT3526: Adding additional media format support to QuickTimeLearn about Adding additional media format support to QuickTime
Handbreak is a very good option to convert files to
iPads, iPhones, etc. It has tried and true presets
for these devices.
As for viewing on Macs, VLC, MPlayer OSX extended are
fairly decent options. As for Perian, it has just been released that
the project is closing down and will no longer be supported.
Also note that mkv is just a container format. The actual video
and audio can be any sort of format, i.e. video could be MPEG-2/4,
VC-1, h.264, etc. and audio aac, ac-3, DTS, etc. Most of these
formats can be handled by the above players, but there are some
that have difficulties depending on hardware.