My husband and I just got back from 11 days in Italy, arriving mid week on Sept 12. The weather was perfect.
We flew into Milan and took a private taxi to Varenna ($140E and well worth it after traveling from the US) which our hotel graciously set up for us. We stayed at Hotel du Lac in Varenna with a superior lake view room ($245E/night, room #35). We would have loved one of the rooms with the balcony but they were already booked. The hotel was great, very nice service, best views in town. I was very glad we booked it over any other hotel in town. I was also glad we stayed in Varenna as opposed to Bellagio which was crowded and packed with tourists. Varenna is a small, quaint town and it's absolutely gorgeous. We went to several of the recommended restaurants in town; the food was good, nothing spectacular, the service was very good everywhere we went. There are lovely views at La Vista at sunset if you have the hotel book a reservation for outdoor seating.
We spent the first three nights in Varenna (had 2 full days) and we would have liked to have stayed another few days. Lake Como far exceeded our expectations in beauty and things to do, we could have easily stayed a week. (This is if you dont go during high season in which case we would avoid Europe altogether.) You are surrounded by the alps! In addition to being able to take the ferry to the various towns, villas, etc., there are tons of hiking options, mountain biking and rock climbing in the area. We were ready to rent a car and head to Switzerland had we not already booked the rest of our trip.
We spent a day in Bellagio and had lunch at the Villa Serbelloni which had incredible views of the lake. Bellagio was pretty, but just ok for me. We elected not to see the other towns as we wanted to enjoy our hotel views. :) We spent an afternoon just relaxing and reading on the hotel balcony taking in the the lake view in the sun drinking prosecco and beer.
We then went by train to Venice (4 nights, stayed in lovely apartment in Dorsoduro) and Rome (4 nights, lovely apartment off Campo di Fiori).
If I could do it again, I would have stayed longer in Varenna AND spent several days in a small town in the alps to enjoy the beautiful outdoors, skipped Rome completely (the crowds, the noise), spent 2 days only in Venice or skipped it (I have been to Venice but my husband had not), and gone to Florence or Siena/some other small town areas.