You'll see it a lot during and after a big weather event as all the "broken pieces" are repositioned to resume normal service.

You'll also see it for cities that have a different number of flights per day on different days of the week such as resort destinations. We have a lot of Caribbean cities that have one, or none, flight per day during the week then multiple flights each on Saturday and Sunday. Crews have to be deadheaded in/out each weekend. I did a Punta Cana, DR trip this summer where we had three complete cockpit crews (six pilots) deadheading EWR-PUJ plus at least one full F/A crew.

Then there are the commuting crews that you mentioned. Only way to tell the difference between commuting and deadhead is to see if they already have their seat assignments or if they're waiting until near the end of boarding to get them. (And that doesn't work if the flight has lots of open seats)