I'm building my first (semi) complex circuit with multiple ICs and I've noticed that the typical or suggested circuit listed in the manufacturer's datasheet is often different from the circuits in breakout boards/shields that use the identical component. I do my best to understand why circuits are constructed the way they are, but it's not always clear to me why one circuit uses x value capacitor while the suggested layout uses y. Is it usually okay to follow the manufacturer's layout or should I follow "real world" example circuits like those found in breakout boards?
The world of electronics is full of compromises and there is more than one way to skin a rabbit. Different engineers have different ways of doing things especially when it comes to capacitors and de-coupling. I always protect inputs from static by putting a resistor in series with inputs and a zener diode to ground other engineers don't, and for a hobbyist it is not required. The fun of electronics is to work out your own solution if you can and not rely on suggested (and that is what they are) pre-designed circuits.
Dead_Ard.
You'll need to give an example if you want specific advice, but one reason might be because the example and breakout board are optimized for a different use. A switching converter module might be optimized for different voltages and currents between the breakout board and a datasheet example.
Often a real like circuit will not require all the things given in the recommended circuit. However if you don't follow the recommended and it doesn't work, you have no comeback on the chip manafacature.
Depends on the circuit.
If I were designing a 30GHz power amp I'd be mad to stray far from the manufacturer's recommended layout . Down to the substrate , the width and thickness of tracks, the plating , and the position of vias.
For a small linear power supply it wouldn't matter much.
Allan
Dead_Ard:
I always protect inputs from static by putting a resistor in series with inputs and a zener diode to ground other engineers don't, and for a hobbyist it is not required.
Protection sometime IS required, and a (5V1)zener/resistor is usually a bad way to protect a high impedance input pin.
Don't assume a pin can take 0-5volt. That's only the case when the Arduino is powered with 5volt.
There are times the Arduino is off, and then the limit is 0.5volt. The zener is then useless.
Leo..
See figure 2
Well, you often don't need to settle on values of caps and other passives until you're putting the parts on the board. So that's something.
Also, differentiate between manufacturer's circuit/schematic, and manufacturer's suggested layout (physical position of the parts/tracks); the latter is a red flag. With regard to suggested external components, read how they talk about the external component selection for clues to the sensitivity to specifics (when they show you lists of specific part numbers, that's a sign, for example 
).
Usually when the manufacturer gives you a layout, it's because the part's performance is layout-sensitive, and if you don't know what you're doing, I'd advise you to shamelessly rip off their layout (that's what it's there for).
With a less sensitive design, they'll usually just give the circuit, and sometimes advise on the layout (eg, "C1 should be positioned as close to the chip as possible"). Often (particularly when they only give one or two circuits) the manufacturers provide an everything and the kitchen sink design, and by studying the datasheet and understanding the purpose of the external components, you may be able to meet your application requirements while still simplifying the design considerably.
Ripping off the design used on breakout boards is also typically a safe bet - provided the breakout board performs adequately. They're often made with low cost as a priority, and better performance may be possible with a more rigorous (and expensive) design.
Things that should make you stick closer to manufacturer's design are high frequencies, radio, switching power supplies, high voltages, and cases where the manufacturer provides a recommended layout. To a lesser extent, high current - but this is usually less complicated.