When planning a VFR flight between two airports the MSFS flight planner (and also Little Navmap and Plan-G) give the frequencies for the departure and arrival airport. But how do I know what the frequencies en route are, in case I want to use FSS for flight following or come across a class D airspace? Default ATC will give them through the menu of course, but how can I know them in advance?

You can do that in LittleNavmap by letting the Map show the Centers. Then you click on the map and get the airspace information and it includes the frequency.