The title pretty much covers it, but to go into more detail:
Various blogs and spec pages have indicated that C and Java are the 2 main native languages used. However, does that actually mean that Native Extensions is limited to this?
In an article here: http://www.adobe.com/devnet/air/articles/developing-native-extensions-air.html
Daniel says 'Although you may be interested in targeting Objective-C, C#, C++, C, or some other language'. Does this mean that C# will be supported? And if so, does that mean that the open source variants Mono and Portable.NET will also be supported for UNIX?
You have to use C to interact with the ActionScript extension classes, but the rest of the extension can be written in any language that you can access from the C code on the specific platform. Objective C, C++, and C# should be fairly straightforward (but I'm not particularly knowledgable on the subject).
Have a look at the .net image encoder example here: http://www.adobe.com/devnet/air/native-extensions-for-air.html for an example of how to use .net in an extension.
(Java can be used directly on Android and Blackberry Tablet OS.)
Can the FlashRuntimeExtension.h be in any way exported to a DLL that C# can read from and extend classes with?