It would be nice if the stamps folder location was stored in the map. When I switch projects, I often forget to reassign the stamps folder and now the 2nd project starts using the tilesets from the first project (same art, so I don’t notice).
Is there a better way to organize stamps for multiple projects?
Tiled will have projects in the future, but now it seems that there are no better way.
There is an issue for Tiled projects, you might want to give it a 
The stamps folder will definitely move to a project setting instead of being global like it is now.
Currently there is in this case no good way, except to pay close attention that you are using the right stamps. The same goes for object templates and external tilesets.