Advantages: Low cost, Linux based, ARM7, Performance, Large number of GPIOs
Disadvantages: Small community, Poorly supported default Linux distribution
The Arduino and the AVR microcontrollers are best for low cost, hard real time, low power, standalone applications, such as wearable electronics, driving LEDs, and simple control applications.
The Netduino and NETMF systems are best at networked complex soft real time control applications. The NETMF microcontrollers are particularly strong if you are interfacing to other Microsoft technologies, such as DWPS or WCF web services.
If your project is graphics intensive the Raspberry Pi is the clear winner. The RPi running Raspbian Linux also makes a great low end development platform.
The BeagleBone Black has the most capable hardware. If you are pushing the limits of performance or available I/Os the BBB could provide the extra capacity you need.