Just wanted to point out, that ERMP does convert MKV.
So far i've converted .avi, .mkv, .ogg and .ogm with it. It can be a bit fiddly, but once you know how it's easy as pie.
The thing with MKV's is that it dosen't mux the soft subs, however that is easily fixed. When you select the save location, also set it to save the out put file as a mkv. Then when it's finished use
MKV Extract to extract the subs file (usually either an ASS or SRT file) and any fonts.
Then use MKV Merge (comes in the above pack) to mux the subs and fonts into the new file.
This results in a new MKV file that is usually around 1mb larger, but retains the fonting and style of the original. Which is something All2Avi can not do.
To convert MKV files though you HAVE to use ERMP internal hali codec, meaning you have to install it at the same time. I usually install everything bar AVISynth.
Bear in mind that there is a bug in the program, for some reason when using 2pass mode it will only convert 4 mkv files at a time (occassionally it may do 5). For some reason after that it crashes and you need to kill it in task manager.
Also with higher resolution files (such as the blue-ray and HD releases) it can be very slow to do the conversion. Longest i had it take was almost an hour with a blue-ray mkv file.