Software :: Converting .mkv Files For ITunes/aTV/iPhone Compatibility?

Yes I know all about Visual Hub, Handbrake, ffmpegX, etc, etc...My question isn't about what tool should be used, but more along the lines of how to use that specific tool as effectively as possible, given that which is most important to me (which I've listed below)...

Without complicating the issue, consider this...

If you had 10 .mkv files (Matroska Multimedia Container files) ranging from 4GB - 7GB in size, and you wanted to convert these files so that they could be viewed in iTunes, on your Apple TV, and/or on your iPhone, how would you do it?

Additional criteria that matters to me:

I don't really care if the movies show up in ultra mega super-duper hi-def in iTunes or on my aTV, just so long as it looks pretty darn good I would really like to avoid having each of these files show up as 4GB m4p files on my iPhone, so that I can avoid having 3 or 4 measly movies taking up all the space on my device...My ideal size range would be anywhere between 500MB (on the very low end of the scale) and 2.5GB (on the very high end of the scale)...somewhere right in the middle would probably be best... I would like to have a single file that was compatible with all of my devices, as opposed to having an aTV version of a movie, and an iPhone version of the same movie

I'd really appreciate any help anyone can offer with this issue (which is completely subjective I realize...but for this reason, the more input the merrier)...and please be as specific as you can regarding the precise settings you would choose for your chosen app, and why you would use them?

I know how to do this about 10 ten ways, and that's the problem...I'd like to know "THE" way (that works best for me of course, and with your input, hopefully I can figure that out!)...