Are there any general rules to follow when choosing between bake and fan bake to cook something in the oven? What effect does each have and what are the advantages and disadvantages of both?
To clarify: forced-air (a/k/a "convection", a/k/a "fan bake") ovens rely on a fan to circulate the air in the oven. The fast-moving air substantially enhances the rate at which heat is transferred to the food. It is particularly good where you want the surface to brown, such as roasts and breads; it is not as good for more delicate items, such as custards and cakes, which can set too quickly or get dried out. For cookies, it depends on what effect you want, but many standard types do well in forced-air ovens because the fan helps ensure that the whole oven stays at a uniform temperature despite the presence of several trays. (Of course, the tray closest to the heating element will still cook faster than the one farthest away, so you will still have to swap them partway through.)
The general rule for using the fan is to set the oven temperature 25 degrees F (15 C) lower than what the recipe calls for using in a regular oven. Even then, don't go strictly by cooking time, as ovens vary; rather, be sure to check on your food regularly to see how fast it is cooking. You may need to cover your food to prevent over-browning, or perhaps adjust the oven temperature.
To add to the excellent answer already provided, I will just point out that the only times I have ever needed to turn the fan off on the connection oven was when baking something fragile. For example phillo dough.
We have a new JGB700 and we have used the convection mode for cooking everything since we bought it, with wonderful results! The oven automatically adjusts the temp to accommodate for the convection cooking difference, so we don't even think about it. Very convenient, and we haven't had anything dry out. Chocolate chip cookies, cupcakes, and a bundt cake all came out great. The french fries and pizza are amazingly good in this mode!