As a general statement, a number of software vendors making non-certified applications are sure to include big bold warnings that the software is only used to increase situational awareness and should not be relied upon for instrument conditions.
For example, the Garmin Pilot Manual has a number of disclaimers (most common sense) to remind you that it is not a substitute for other systems.
That said, as Qantas 94 Heavy pointed out, the answer is quite different for certified avionics, and that depends on which part of the FAR the aircraft is being certified under.
If you make something like an E6B app, you're probably in the clear. After all, you would have just made some calculator with preprogrammed functions.