Answer:
It depends on the type of baking being done. The most important thing the bakery needs is to get certified by a reputable kashrut organisation. Without proper certification, it is illegal for any food producer to call its products kosher.
The kashrut organisation will work with the company to make sure it follows all the requirements of kashrut. Some of the basics are:
1. Are the baked goods all going to be pareve (no dairy OR meat [eggs are pareve]), dairy, or does the bakery want to produce both dairy and pareve items.
2. If the bakery is going to produce both dairy and pareve products on a daily basis, there must be separate equipment including mixers, bowls, utensils, and ovens for. One set being used only for dairy and the other for pareve.
3. If the owners are not Jewish, they will most likely be required to have a 'mashgiach' present at all times of operation. A mashgiach is a supervisor who is a religiously observant Jewish man and who will work for and be paid by the bakery owners.
4. There are ways to have the bakery open during Shabbat (Friday sundown through Saturday sundown), however, no food production can be done during Shabbat.
5. All products used in the bakery must be certified kosher.