As these separate sub projects interact, then they need to move in lockstep, and you need to tag/branch/release the C#/Java/whatever components together. If they're unrelated then I would advocate (perhaps) separate repositories, or separate directories within the same repository. But not branches or tags.
Branches are used to manage different development streams on the same codebase. Tags are used to indicate a particular point in the project's evolution.
I think the programming language is irrelevant. Ask yourself what your releasable is, and how you need to manage this. I've done this successfully in the past with projects incorporating Java and C++, and the language is not the issue - it's keeping the components in sync that you need to manage.
I wouldn't necessarily create a new top-level directory per language. What happens if your Java component suddenly requires a JNI layer ? It strikes me that the implementation is reflected in the top-level directory structure, and that shouldn't really be a concern.