Lets say for now its PIC, but plans to migrate the micro to moto or other.
I know of the clamping diodes, but wasn't sure if it was 'recommended practice' to trust them.
Sceadwian: I haven't seen that appnote but I have heard similar stories. I'll take a look for it.
My 5V ADC signals are all going through a voltage follower opamp but right now my 5V digital wires are just direct to the micro from the connector, I'm sure thats not exactly correct.
As far as my outputs go I have a decent relay driver, but lets say no more then 25ma for 12V out. I'm guessing a simple transistor or fet but I would like it to be at least short protected, thats the type of thing I'm curious about.
I've been looking around for app notes and schematics but haven't come up with much,