How about using a DelegatingHandler to override the acceptheader?
public class MediaTypeDelegatingHandler : DelegatingHandler
{
    protected override async Task<HttpResponseMessage> SendAsync(HttpRequestMessage request, CancellationToken cancellationToken)
    {
        var url = request.RequestUri.ToString();
        //TODO: Maybe a more elegant check?
        if (url.EndsWith(".json"))
        {
            // clear the accept and replace it to use JSON.
            request.Headers.Accept.Clear();
            request.Headers.Accept.Add(new MediaTypeWithQualityHeaderValue("application/json"));
        }
        else if (url.EndsWith(".xml"))
        {
            request.Headers.Accept.Clear();
            request.Headers.Accept.Add(new MediaTypeWithQualityHeaderValue("application/xml"));
        }
        return await base.SendAsync(request, cancellationToken);
    }
}
And in your configuration:
GlobalConfiguration.Configuration.MessageHandlers.Add(new MediaTypeDelegatingHandler());
And your controller:
public class FooController : ApiController
{
    public string Get()
    {
        return "test";
    }
}
And if you go to http://yoursite.com/api/Foo/?.json should return:
"test"
While http://yoursite.com/api/Foo/?.xml should return
<string xmlns="http://schemas.microsoft.com/2003/10/Serialization/">test</string>
Edit:
Note that you still need to handle the route parameter input, since the controller doesn't expect the .json-parameter. That's why the ? may be necessary.