What would I call a program that was developed specifically for a company?
Solution 1:
The answer depends on the sentence you're using, but there are a few ways to say what you mean.
Software used and developed within an organization is often called either in-house or proprietary software, as opposed to shrink-wrapped of off-the-shelf software.
Work done to develop software for a client is often called contract work, and is clearly distinguished from school assignments, side projects or pet projects.