If you haven't explored the possibility of travelling all over Europe with a Eurail pass, then you're really missing out on a great opportunity. Train travel is incredibly comfortable, scenic, affordable, and dependable. We're going to Munich for Oktoberfest at the end of September and then on to Prague before heading back to Germany, using the train as our main mode of transport.
Other thoughts...last year we went on a self-guided bike tour through Burgundy. Relatively easy biking, which is good since we stopped every hour in another winery and tried their wares.
Barcelona is gorgeous at that time of year. The tourists have thinned out but the weather is still comfortable. There are worst ways to spend a few days than checking out Gaudi's creations (especially Sagrada Familia) and hitting every tapas bar along Las Ramblas.
Another thought...use the ferry system in Greece and explore the islands - but not the usual suspects like Mykonos and Ios. For our honeymoon we took a sailboat and went to islands like Kifnos, Kea, Syros, and Sifnos. Some of these islands are too small to accept cruise ships but all are accessible by small boats. That's where you see real Med island life.
Yeah - that's it. Planes, trains, ferries, and bicycles. Do it all. Sept/Oct is a great time to see Europe!!