If you put your preferences into a list, it might become easier.
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));
This will put all items not appearing in preferences in front because IndexOf() returns -1. An ad hoc work around might be reversing preferences and order the result descending. This becomes quite ugly, but works.
IEnumerable<String> orderedData = data.OrderByDescending(
   item => Enumerable.Reverse(preferences).ToList().IndexOf(item));
The solution becomes a bit nicer if you concat preferences and data.
IEnumerable<String> orderedData = data.OrderBy(
   item => preferences.Concat(data).ToList().IndexOf(item));
I don't like Concat() and ToList() in there. But for the moment I have no really good way around that. I am looking for a nice trick to turn the -1  of the first example into a big number.