Quite a few products that are essentially free make their money by commercial licensing (or support licensing).
Another method I can think of is by including desirable premium features that essentially "subsidize" the free version.
Since it is a desktop app, I'd steer clear away from advertising. I personally think Microsoft has self-sabotaged their Start menu by putting ads on it. I completely ignore the screen and never use it because I don't have the patience to determine what elements are actually apps I have, and which are apps they're trying to hoist on me.