You need to use
SelectMany to concatenate result sets.
var items = employees.SelectMany(e => e.Orders.Select(o => new Item(e.ID, o.ID)));
The extension method you're looking for is called "SelectMany": http://msdn.microsoft.com/en-en/library/system.linq.enumerable.selectmany.aspx
Have a look at
Enumerables.SelectMany(), see the example in this Stack Overflow question.
For what it's worth, this can be written somewhat more succinctly and clearly in LINQ syntax:
var s = from e in employees from o in e.Orders select new Item(e.ID, o.ID);
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