Samsung acquires LCD panel manufacturing JV share from Sony - ElectroIQ
The above article is about Sony and Samsung panels. ;) As far as "3rd party" panels go, I would probably say Samsung is one of the best "3rd parties".
If you need something that can understand the MKV container and other uncommon containers/codecs, you can always purchase a Roku box. Granted this is something that would add to the price, whereas the Panasonic may come with the feature built-in.
FYI: IPS alpha, from what I can tell, is no different than regular IPS except that it supposedly has improved viewing angles. Sounds like marketing stuff. Keep in mind that the Sony uses an S-IPS panel, which is actually better in picture quality than the IPS panels. It's possible that the Panasonic uses an improved S-IPS panel in their set as well. I'm more familiar with the North American models.
It doesn't sound like you will be doing any gaming on either of the sets. So I would really break it down to personal preference. Since you seem to like the Panasonic most, then that is what you should go with.
Keep in mind that when you look at TVs, usually you want to look at how well they emulate black levels (without over doing it). It helps to compare them to a plasma. And you also want to look for color accuracy, and not how vivid the set is.
Most TVs on the sales floors are set to look the brightest they possibly can, and in just about any normal viewing environment, this will burn your eyes out of your skull.
So basically, I think you'll be happy with either set. But if you think the picture looks better on the Panasonic, and it has the ability to play your desired formats without purchasing some extra component, then I would go with the Panasonic.