There are numerous ways to do this. This is arguably one of the easiest type of factories to make. Multiple mods all have ways of doing automatic crafting. Buildcraft has the auto-crafting table. Thermal expansion has the cyclic assembler. GregTech has the electric crafting table Mk III. You could also go completely overboard and use the molecular assembly chamber from Applied Energistics. All of these will take items from the input and auto-craft them into their output using the crafting recipe.
There are 2-3 steps to building a bread farm. The first is growing the wheat and/or barley (and harvesting/planting). The next is turning the wheat into flour and then baking, or turning the wheat into bread directly. The last is subjective, and that is automating the item transportation from the farm all the way to your storage system.
This can be done with varying levels of automation. To start off, you might just automate the turning of wheat into bread directly. This could be as simple as a couple of hoppers (to move items into and out of the crafting table), the buildcraft auto-crafting table, and a couple chests (input and output). Next, you might use wheat converted to flour in a crafting table, then baking the flour in a furnace to increase your bread yield from 3 wheat per bread to 1 wheat per bread. Now, you not only have to automate the crafting, but also supply fuel to the furnace.
Things can get more complex from there as you automate the different sections. As casilleroatr pointed out above, you can automate the actual farming. This can again be done using a bunch of different mods (forestry, minefactory reloaded and thaumcraft come to mind most readily). You can also automate the item transportation and move your resources from the farm to the end storage. As most mods have an energy requirement to operate their machines, as you automate different sections, not only do you have to build the farm, you now also have to build the engines and generators required to power the machines. This starts greatly increasing the complexity and required infrastructure.
Start with what you know. Add on from there. You can get overloaded if you try to do it all at once, as there are lots of contingencies that need to be accounted for as the automation gets progressively more advanced and integrated. The ultimate in automation/integration is you doing nothing while your automated system takes care of your farming, harvesting, fuel production, bread production and storing the finished product--all the while making it robust enough to handle excess items, energy shortages, and able to run without additional maintenance. In some worlds, I never make it this far, and instead settle for semi-automatic, as it leaves time to devote to other sections of minecraft like exploring or building.
If you have difficulties, let us know what items/mods you are working with, and we can further assist if necessary.