As a provider of Industrial PCs, I have found that ATX Motherboards and Single Board Computers (SBC) have some distinct differences that Industrial Computer System users should be aware of prior to making a purchase.  With variables such as peripherals, I/O, ease of access and form factor to keep in mind, it is important to be well-informed about which type of computer is best suited for your system requirements.
There areATX Motherboard certain applications in which ATX Motherboards are the best answer. For the customers focused on an economical configuration, fewer I/O slots and ease of access, ATX Motherboards are a nice fit. They create great airflow due to more chassis space and provide better cabling options to the end user. You can also still find ATX Motherboards with legacy ISA slots included, are necessary for some projects.
There are other times when a Single Board Computer is the go-to option. An SBC provides the user with access of up to 20Single Board Computer I/O slots, allowing them to configure their system with a predetermined amount of ISA, PCI, PCIe and PCI-X slots. Customers looking for ISA slots are also better off with an SBC since most ATX Motherboards containing ISA slots have been discontinued. When you are in a space crunch, SBCs are great with desktop, wall mount and “shoebox” chassis, allowing for a smaller form factor solution.
To summarize, ATX Motherboards and SBCs provide the following for Industrial PCs:

ATX Motherboards:

  1. Economical
  2. Contain fewer I/O slots
  3. Ease of access
  4. More room for air flow
Single Board Computers:

  1. Larger amount of I/O slots
  2. Access to Legacy ISA slots
  3. Desktop, Wall Mount and “Shoebox” chassis
  4. PICMG 1.0 and PICMG 1.3 compatibility