Easily Batch Convert avi, wmv, mov, flv to MP4

Ok, so I want to somehow convert my massive video collection to MP4. I've picked MP4 because it seems to be universally compatible with items like, quicktime, my iPhone, and my PS3. It also contains MetaData that I can then manipulate and edit with MetaX.

But this is what I am looking for specifically:

1. Something that can do batch processing. Maybe even with different source formats (select a group of avi and wmv files).
2. Something that has pretty much every codec built in. I don't want to batch convert like 50 files and then come back later and find that one of the files didn't have the audio codec, but I've already deleted the source.
3. Something that has a maximum resolution threshold. This seems to be a tricky one. The goal of this is to reduce a 30 minute show to something under a 1 Gig per-say (just a random example). Point being, I don't need HD resolution for everything, and I want to say that if this movie is above a certain resolution, or FPS, or what have you, shrink the size down a bit. But don't force other movies that are lower or that aren't at the same proportions into that format.
4. Something that's stable and gives a good success rate. A couple years back I used Automater to direct Quicktime to convert wmv and avi to mov files, and it seemed ok. I loaded them into iTunes and started to add metadate. Problem was, some (not all, but a lot) would crash at certain points during playback.

Any ideas?
4.

theLimit said:

HandBrake meets all of those requirements, iSquint might do what you want as well.

Click to expand...

1. Well HandBrake has a queue, yes, but one has to add each file one by one, adjust according, then add to the queue. Not exactly batch conversion, unless I'm missing an option somewhere.
2. Yes, HandBrake is great with source codec, and I'm sure there's very few files I could find that it couldn't read.
3. Again, don't see a maximum resolution, bitrate, etc threshold. I want to say, if the video is over 480dpi, bring it down to 480dpi. If it's under, just leave alone.
4. HandBrake is about as stable as they come, yes.
*5. Another feature that I didn't mention, is saving the video in it's original location. Meaning if I take a TV series and select multiple seasons from folders, I want all those videos to remain in the same source as the original. iSquint says it can do this automatically, but asks for a specific "saving in" path.

iSquint I downloaded and looked through a bit. It has the ability to batch convert by just dragging all the files, which is great, but then it looks like it will save all those files in one place, regardless if they are coming from different folders. It's advanced settings are a bit basic too, and it doesn't look like it has threshold limit conversions which is what I'm looking for, but I'll look at it some more. The main flag is that support for this program was stopped a couple years ago, so will it handle all of my current video, and will it do it with out any glitches that I may not realize until later on when I've deleted the source videos?

I can't be the only one trying to do this, I'll search more on macrumors, but anyone have a guide to massive video conversion, possibly using HandBrake either on macrumors or somewhere else...a recent guide too?

I found Video Monkey which looks promising. Can just drag and drop all the files you want for batch converting. Then in a large grid shows frame size, framerate, bitrate, and audio quality for each file, along with their duration and expected output file size. There's plenty of default output setting, one being for all apple devices. However the Advanced tab and the convert to all the other default settings are greyed out.

Anyone have any specific experience and opinion with this software?