A
B
A
C
B
C
D
E

firstPref = 'A';
secondPref = 'B';
thirdPref = 'C';

A
A
B
B
C
C
D
E

List<String> data = new List<String> { "A","B","A","C","B","C","D","E" };
List<String> preferences = new List<String> { "A","B","C" };

IEnumerable<String> orderedData = data.OrderBy(
   item => preferences.IndexOf(item));

IEnumerable<String> orderedData = data.OrderByDescending(
   item => Enumerable.Reverse(preferences).ToList().IndexOf(item));

IEnumerable<String> orderedData = data.OrderBy(
   item => preferences.Concat(data).ToList().IndexOf(item));

string[] svals = new string[] {"A", "B", "A", "C", "B", "C", "D", "E"};
    List<string> list = svals.OrderBy(a => a, new CustomComparer()).ToList();

    private class CustomComparer : IComparer<string>
    {
        private string firstPref = "A";
        private string secondPref = "B";
        private string thirdPref = "C";
        public int Compare(string x, string y)
        {
            // first pref
            if (y == firstPref && x == firstPref)
                return 0;
            else if (x == firstPref && y != firstPref)
                return -1;
            else if (y == firstPref && x != firstPref)
                return 1;
            // second pref
            else if (y == secondPref && x == secondPref)
                return 0;
            else if (x == secondPref && y != secondPref)
                return -1;
            else if (y == secondPref && x != secondPref)
                return 1;
            // third pref
            else if (y == thirdPref && x == thirdPref)
                return 0;
            else if (x == thirdPref && y != thirdPref)
                return -1;
            else
                return string.Compare(x, y);
        }
    }

List<string> data = new List<string> {
	"E", "B", "D", "A", "C", "B", "A", "C"
};
var preferences = new Dictionary<string, string> {
	{ "A", " 01" },
	{ "B", " 02" },
	{ "C", " 03" }
};

string key;
IEnumerable<String> orderedData = data.OrderBy(
	item => preferences.TryGetValue(item, out key) ? key : item
);