To play Bakery Story effectively, it is important to pick a strategy that will help you achieve your goals - whether it is to earn coins, XPs, gems, etc.  Since the type of food you prepare will determine how quickly you accomplish your chosen task, choosing dishes is an important part of the game.  Prioritize what you want currently and follow the suggestions below:

Earning coins:
Since it's not practical to play Bakery Story constantly for 24 hours a day, it is best to choose among alternative dishes for a given length of time that will provide the most amount of coins.

The dishes that provide the most amount of coins per minute of preparation time are the ones that are the fastest to prepare.  So if you are wanting to earn coins fast and are willing to play Bakery Story for hours non-stop, start baking some Brownies and Chocolate Cookies.  

Earning XPs:
If your goal is to simply to level up in Bakery Story, simply choose dishes that give you the maximum amount of XPs - which can be found under the description of the dishes in your "Cookbook."

Earning gems:
If you are interested in getting Forever appliances, Sonic appliances, or other premium furniture and decorations, you will need to either earn gems or purchase them.

Though a slow process, you can earn gems by simply getting promoted for preparing/serving foods.  Keep in mind that you will not earn gems every single time you get promoted - only after the second and fourth promotion.