Based on what I understand from your question, you could try something like this:
//Category implementation
public class Category
{
    public List<Category> SubCategories { get; set; }
    public int CategoryID { get; set; }
    public static int count = 0;
    public Category()
    {
        SubCategories = new List<Category>();
    }
    public void Add(Category cat)
    {
        SubCategories.Add(cat);
    }
    public IEnumerable<Category> AllSubCategories()
    {
        var stack = new Stack<Category>();
        stack.Push(this);
        while (stack.Count > 0)
        {
            Category cat = stack.Pop();
            yield return cat;
            foreach (Category nextCat in cat.SubCategories)
                stack.Push(nextCat);
        }
    }
}
...
//Testing the code
Category top = new Category() { CategoryID = 1 };
top.Add(new Category() { CategoryID = 2 });
top.Add(new Category() { CategoryID = 5 });
top.Add(new Category() { CategoryID = 3 });
top.Add(new Category() { CategoryID = 1 });
top.Add(new Category() { CategoryID = 2 });
top.Add(new Category() { CategoryID = 4 });
Category tmp = new Category() { CategoryID = 1 };
top.Add(tmp);
tmp.Add(new Category() { CategoryID = 1 });
tmp.Add(new Category() { CategoryID = 7 });
tmp.Add(new Category() { CategoryID = 6 });
Category tmp2 = new Category() { CategoryID = 7 };
tmp.Add(tmp2);
Category tmp3 = new Category() { CategoryID = 4 };
tmp2.Add(tmp3);
Category tmp4 = new Category() { CategoryID = 3 };
tmp3.Add(tmp4);
Category tmp5 = new Category() { CategoryID = 1 };
tmp4.Add(tmp5);
Category tmp6 = new Category() { CategoryID = 9 };
tmp5.Add(tmp6);
var Result = top.AllSubCategories().GroupBy(c => c.CategoryID).Select(g => g.First()).ToList();
Cheers
EDIT #1: I think I should give credit to Jon Skeet for this idea: https://stackoverflow.com/a/2055946/172769
Just in case anyone is wondering where it came from.
EDIT #2: Based on comments from Eric Lippert about bad performace of nested iterators, I changed my code to use an "unwind to stack" method that I got from: https://stackoverflow.com/a/1043363/172769