The tiny breadboard seen here is from Adafruit and was used to layout the parts specifically for Adafruit's shield, which is more of a printed breadboard design - if it could fit on the breadboard, it could fit on the shield. The empty side of the breadboard is where the other sensors and indicators belong.
With Adafruit's shield we ran into a clearance issue between the proto shield and the Arduino ethernet shield. The ethernet jack is 0.5" tall and Adafruit's shield kit does not come with stackable header pins - the pins it does comes with are not long enough to make the connection when stacked on the ethernet shield. Fortunately, we roughed the proto shield parts into place with the Uno and ethernet shield before soldering the kit together, saving us from desoldering the proto shield to add stackable pins.
The official Arduino proto shield does not have this clearance issue and we'll test the Make shield later (since it comes with stackable header pins, we can't immediately see it having any issues). All three shields are capable of being placed between the Uno and the Ethernet shield making the clearance seemingly irrelevant. However, if you chose to solder the DHT sensor directly into the proto shield (flat, unlike the picture), and then sandwich the shield between the Uno and Ethernet, your temperature and humidity readings could become skewed by the ambient heat generated from the other shields. This means you would have to use extension wires to move the sensor to the enclosure and if you don't hard solder the extension cables in, instead choosing to use removable connectors, you might be presented with clearance issues all over again. In the end, simply adding stackable header pins was the easier option.
The Adafruit's shield is very simple to put together and barring the (easy to resolve) header issue, worked well. Because the Adafruit's proto shield is similar to a breadboard it is more intuitive to setup a circuit design from the breadboard vs. the Make or Arduino proto shields, which we'll discuss in more detail later.
Using Arduino with Aquaponics is covered in our upcoming book Automating Aquaponics with Arduino and companion kit.