Using ASP.NET Web API along with ASP.NET Identity 1.0, you can use this extension method to retrieve the currently signed in user:
var id = Microsoft.AspNet.Identity.IdentityExtensions.GetUserId(User.Identity);
But in ASP.NET identity 2.0 alpha, you can override the type for the ID field. The example given by Microsoft shows setting this field to be an int. But this extension method seems to be hardcoded to return a string even in the alpha:
How can you retrieve the (int) identity of the currently logged in user from within a Web API controller when using ASP.NET Identity 2.0 alpha?