Is it possible to configure OwnCloud in such a way that different Clients share different folders with OwnCloud? The content of the folder on Client1 should not be synced to Client2.
Yes this is possible. You can set up any directory for synchrisation with the client. Additional sync directories can be configured by right-clicking on the tray icon and selecting "Add folder"... simply enter a different directory as needed on each client! The default sync directory "clientsync" is configured during client setup, but you can remove this as well in the dialog that pops up when you select "Open status" from the context menu
Tested with ownCloud 4.5.8 (should work the same with the new 5.0.3) and client 1.2.3.