Just add up the calories for each ingredient separately. The cooking method can change the calories, but not enough that it is worth worrying about (in the end, all this calorie counting is just an estimate anyway). Of course, if you cook something in oil, you have to remember to add the calories in the oil to your analysis as well.
There are several recipes that will tally the calories in a recipe for you (you enter the ingredients and the website adds up the calories). Try
www.fitwatch.com or
www.nutritiondata.com. Fitday will let you create custom foods, but I don't know if it will actually tally up the calories for you.