Massive Handbrake batch processing - need guidance

I'm basically hoping that someone could put themselves in my situation and answer the following question:
I plan on deleting my source files when I'm done, so I don't want to screw this up. Any suggestions would be greatly appreciated... Thanks!

Didn't like the answers you got in the HandBrake forum?

I liked those answers just fine, but past experience has shown that there are some really smart and helpful people on these forums, and I figured it couldn't hurt to get more feedback on the issue at hand than I could get from just a single forum.

Given my situation, and given then tragedy it would be to mess things up, I figured more feedback just might be warranted in my case.

It's tough to give good advice here with so little information. As was discovered in the HB forum, many of the files just need remuxing and possibly audio reencoding rather than degrading the video by transcoding.

Yeah... I think this is going to be the road I'm going to head down, at least for making my .mkv files iOS compatible. I'm still scratching my head on how to handle the hundreds of avi, mov, wmv movie files I have that need to be iOS compatible but can't be re-muxed.

Basically I'm lazy, and I know that you could always get a better result fine-tuning each individual movie file by encoding, then tweaking settings and re-encoding, etc... but there is no chance I'll be doing that because I work a day job and have two kids that would like to know their father.

Needless to say, I am in search of the best batch-processing solution I can find to ensure that my movies are as close to the original quality as possible, while at the same time being iOS/aTV compatible.

You're asking for fundamentally opposite things - the best, without any effort. You're also asking for things ("as close to the original quality as possible, while at the same time being iOS/aTV compatible") you probably don't really want - to achieve this literally you'd suffer massive file sizes.

I'd say Apple TV 3 preset is your best compromise.