Aseprite came to mind for me, too. Then again, Aseprite is aimed at artists rather than programmers. I'd argue that most people who use it don't want to go through the hassle of compiling it themselves – compiling software can be a daunting task. I have the feeling that a similar business model ("free on github if you're willing to put a little work into it, paid in stores if you prefer comfort") wouldn't work as well as it does for Aseprite if the software would be aimed at programmers.

Ardour comes to mind. They don't even assist any building steps and just direct people to the paid download version.

Simple Mobile Tools in Android too. Paid in Play Store, free in F-Droid. Simple Mobile Gallery is the top notch gallery app on Android.

Same for the XMPP based chat app for android, Conversations (although F-droid already provides a compiled package, so users don't really have much incentive to buy the Play Store version).

Lovely app too. I looked at the effort required to compile and just paid the AU$28. Very happy.