I've seen it be done and have done it two ways.
Assume an agile methodology... but I guess this can apply to any sdlc method.
1) Your customers help you prioritize features. Be they a group inside the enterprise or beta users or real users... You'll need to communicate with them and find out what features they want first.
2) You will prioritize based on a Use Case/Benefit/Value Proposition... Build features and capabilities that will meet that benchmark.
Beyond that... you built, test, measure.
Hope that helps.