For JavaScript, you're probably best off just using HTML5 IndexedDB. Unfortunately, that is not directly available to other languages.
There is a stock second option: Windows has an integrated embedded database in form of Extensible Storage Engine. It's a relatively simple ISAM DB (no SQL, you need to query indices directly). It is a whitelisted API for Metro applications.
Using it from C++ is straightforward - just #include <esent.h>
and go ahead. For C#, you'll need to use P/Invoke. For JavaScript, you'll need to write a wrapper around ESE API using C++/CX.
Yet another option is to take SQLite and make it compile (and pass app certification check for banned APIs) for WinRT. You'll need to make some tweaks to the code to get it to work, but there aren't many.