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Two years ago I've made a short movie with RAW and non-RAW footage from 5D Mk II (I had only one fast card, so I couldn't shoot it RAW etirely) and for me it's very cleraly visible which scenes are shot in RAW, and which in compressed format. I had also made an experiment: I had shown that movie to a few persons (definitely not film or color specialists), and I asked them to try to recognize footage shot in "better format", as I described RAW to them. The results were quite interesting. I got on average 75% correct guesses which takes were shot in RAW, and which not. And the "mistaken" takes were mainly H.264 shots with not so much motion - compression artifacts in them were not so obvious, and they were taken as a RAW footage by the viewers.

So if you mix in-camera H.264 with RAW, it will be probably recognizable for some viewers, but of course it does not mean, that you shouldn't do that and your movie won't benefit on it (e.g. if a second camera will allow you to get a different angle with more interesting framing and so on). In "Phantom Menace" they mixed 35mm film with footage from very early HD camera (which - again - was quite visible for me), but the movie was in theaters, and made a lot of money.

Processing CinemaDNG files in ACR may also help. It has embedded some algorithms that try to remove bad/hot pixels from raw files.

RAW files from 5D Mk III definietly will be god enough to show them on a big screen, but H.264 compressed video also should be suitable for that (I'm assuming proper lighting on the set etc.). Shane Hurlbut recorded about 70% of the "Act of valor" with 5D Mk II in compressed format, and the movie had theatrical release.

But I would recommend shooting in RAW (when you once try it, you don't want to use H.264 anymore). With RAW files you will have lots of options when it comes to color grading, and you will get more sharp and clean files compared to those compressed in camera.

Probably you should enable raw_rec or mlv_rec module in Modules tab first (enabling mlv_rec with mlv_sound module gives you ability to record sound with raw video). Then, after restarting the camera, you will see RAW Video option in Movie tab. It will be also possible to select resolution of the raw file in this option dialog window.

I had written an e-mail to KB about compatibility, I'm waiting for their reply. Unfortunately I live in Poland, so sending anything back and forth to USA is a very bad idea.
Yes, I know about UDMA-7 readers issue, I have Transcend RDF8K and it works well with my KB 64GB 1000x.
How about KB 128GB 1066x and 5D Mk II? Would it work? Again, lots of mixed reviews here, but most of them about performance with 5D Mk III, not Mk II.
I think, that it would be good idea to create a compiled table of different cards reports, such as "current RAW video capabilities" on google docs. Maybe in the future I will have a time for that tedious task...

Thanks for reply. I'm buying cards from Amazon.de and they don't have 128 GB 1200x version (was such card ever produced by Komputerbay?). KB 128 GB 1066x is slightly more expensive (2 EUR difference), but I understand, that it's 100% compatible/bootable with 5D Mk II?

What is the current status of compatibility of KB 128GB 1000x and 1050x with 5D Mk II? Is Magic Lantern bootable on these cards? Are they fast enough to record continuously MLV with sound in 1856 x 790 (or in higher resolutions)? I'm planning to buy one of these cards and I have found lots of mixed reports about them. Some claimed that they don't work, others they do...

[Update 2:]

Hi!

First of all I would like to thank everyone involved in ML development. What a fantastic piece of software!

And now let's get down to the business. Since I've started recording raws with my 5D Mk II I have strange problem with audio included in MLV file. At the beginning of the wav file (extracted with different versions of raw2cdng) I get awful noises. Sometimes I get this noises also in the middle of the whole wav file, which very often makes it completely unusable, especially when I record dialogs. Not every single file recorded is noisy, it happens more or less randomly, but mostly after camera restart or changing the CF card.

Here is the link to the sample noise from my video - https://www.youtube.com/watch?v=mSLVuziOsTI&feature=youtu.be

I found similar topic, but there were no answers - http://www.magiclantern.fm/forum/index.php?topic=13800.msg133275#msg133275

I use ML Nightly.2015Jan03 version on 5D Mk II. My audio settings:
Analog Gain: 26 or 29 dB
Digital Gain: 0 dB
Input source: L:int R:ext (my external mic is Rode VideoMic)
Wind Filter: OFF
Headphone Mon.: OFF

So how can I fix this?

Update: I have installed latest Nightly Bulid (2015Jul02) and I still get those noises. I have also tested MLV recodring without external mic and it didn't help.

Update 2: Mystery finaly solved: it's strange, but when I record MLV with sound on different CF card (meanwhile I have bought two Komputerbays 64GB 1000x) I don't get this awful noises. So my guess is, that the old card (Transcend 64GB 1000x) was not fast enough to record audio simultaneously, and from time to time generated those noises. On new cards I have also longer recording times in higher resolutions, so I think that the whole problem has something to do with a card speed.