Software Options for Program Management

I'm trying to get a better understanding of what goes into supporting field work for global development programs from a software perspective. I imagine that there's at least some data entry and digital recordkeeping that goes into keeping track of progress and communicating updates internally. I've heard some people talk about using spreadsheets or donor/M&E tools like DHIS2, but the sense I get is that for the most part programs are relying on custom adaptations of software that doesn't quite fit right (Or multi-platform franken-stacks via a tool like OpenFn). Is that an accurate read? 

What tools have people seen used in practice? What were their limitations and strengths?