I'm just wondering what would be considered industry practice of communicating between multiple micro controllers on the same pcb for instance when the digital i/o's or analog ins have been used.

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    \$\begingroup\$ How many microcontrollers? What's the max data rate that you are expecting? \$\endgroup\$ – Nick Alexeev Mar 5 '15 at 22:56

There are numerous standardized link layer interfaces available - typically at least I2C, SPI, UART and parallel - but to the best of my knowledge there are no uniformly accepted standards for higher level protocol layers for inter-MCU comms. If you need to do it then you just roll your own to suit your particular requirements.

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