For others. You have to include properties in car that holds the value of the Id in Country and LicensePlate.

    [Serializable]
    public class Car
    {
        private LicencePlate _licencePlate;
        private Country _country;

        public LicencePlate LicencePlate
        {
            get { return _licencePlate; }
            set
            {
                _licencePlate = value;
                LicencePlateId = value != null ? value.Id : 0;
            }
        }

        public Country Country
        {
            get { return _country; }
            set
            {
                _country = value;
                CountryId = value != null ? value.Id : 0;
            }
        }

        public int LicencePlateId { get; private set; }

        public int CountryId { get; private set; }

        public string Color { get; set; }

        public Car()
        {
        }
    }

    [Serializable]
    public class LicencePlate
    {
        public int Id { get; set; }
        public string Plate { get; set; }
    }

    [Serializable]
    public class Country
    {
        public int Id { get; set; }
        public string Name { get; set; }
    }

    [Serializable]
    public class LicencePlateMapping : EntityConfiguration<LicencePlate>
    {
        public LicencePlateMapping()
        {
            HasKey(l => l.Id);
            Property(l => l.Id).IsIdentity();
            Property(l => l.Plate).IsRequired();
        }
    }

    [Serializable]
    public class CountryMapping : EntityConfiguration<Country>
    {
        public CountryMapping()
        {
            HasKey(c => c.Id);
            Property(c => c.Id).IsIdentity();
            Property(c => c.Name).IsRequired();
        }
    }

    [Serializable]
    public class CarMapping : EntityConfiguration<Car>
    {
        public CarMapping()
        {
            HasKey(c => new { c.CountryId, c.LicencePlateId });

            Property(c => c.Color);

            Relationship<LicencePlate>(c => c.LicencePlate).IsRequired().HasConstraint((c, l) => c.LicencePlateId == l.Id);
            Relationship<Country>(c => c.Country).IsRequired().HasConstraint((car, country) => car.CountryId == country.Id);
        }
    }

OK this helps .
But what if, to build on your example:

public class LicensePlate{
public int ID {get;set;}
public string Plate{get;set;}
}

public class Country{
public int ID{get;set;}
public string Name{get;set;}
}

public class Car{
public LicensePlate LicensePlate{get;set;}
public Country Country{get;set;}
public int SomeProperty{get;set;}
}
So you’ll have a join table with extra fields.

To map the Car I would expect: HasKey(c => new { LicensePlate_ID = c.LicensePlate.ID, Country_ID = c.Country.ID });

However, the key expression is not valid.

Greets,
Arne