A workaround that will recognise when a SingleResult type does not contain any results and replace it with a 404 instead of throwing a SerializationException.

ReplaceNullContentWithNotFoundAttribute

        internal class ReplaceNullContentWithNotFoundAttribute : EnableQueryAttribute
        {
            public override void OnActionExecuted(HttpActionExecutedContext actionExecutedContext)
            {
                base.OnActionExecuted(actionExecutedContext);

                HttpResponseMessage httpResponseMessage = actionExecutedContext.Response;
                if (httpResponseMessage.IsSuccessStatusCode && IsContentMissingValue(httpResponseMessage))
                {
                    actionExecutedContext.Response = actionExecutedContext.Request.CreateResponse(HttpStatusCode.NotFound);
                }
            }

            private static bool IsContentMissingValue(HttpResponseMessage httpResponseMessage)
            {
                var objectContent = httpResponseMessage.Content as ObjectContent;
                if (objectContent == null)
                {
                    return false;
                }

                var type = GetType(objectContent);
                return type == typeof(SingleResult<>) && objectContent.Value == null;
            }

            private static Type GetType(ObjectContent objectContent)
            {
                var type = objectContent.ObjectType;
                if (type.IsGenericType && !type.IsGenericTypeDefinition)
                {
                    var genericTypeDefinition = type.GetGenericTypeDefinition();
                    type = genericTypeDefinition;
                }
                return type;
            }
        }

@andygjp I saw your comment on SO and I dont have enough rep there to ask you how to implement your code in a simple get call like this, also @taehtinen

    [EnableQuery]
    public SingleResult<Apple> Get([FromODataUri] int key)
    {
        IQueryable<Apple> result = db.Apples.Where(p => p.AppleId == key);
        return SingleResult.Create(result);
    }