In Venice we stayed at Pensione Guerrato. We enjoyed it there and thought the location was great. For Venice the price was really good too. It was fun to wander around the market next to the Pensione and see some unfamiliar looking things.
In Varenna we stayed at the Orange House. It's a 2 room B&B that is run by a lovely couple. They live off site. The upstairs room is ensuite and the downstairs room has a private bathroom across the hall. There is also a living/dining area where breakfast is served. The price is excellent. It is an easy walk from the train station and the ferry. One of my favorite things we did during our 3 week trip in Italy was to take a cooking class at Il Caminetto. They will come pick you up in town, usually at the ferry. When they found out we were staying at the Orange House they picked us up there. Plan to spend all day, but for a very reasonable amount of money you will be wined, dined, entertained and learn how to cook some delicious Italian dishes.
In Florence we stayed at Il Bargellino. It was an easy walk from the train station and to all the sites we saw in Florence. They don't serve breakfast. The room did have a small refrigerator, which was not common amongst the places we stayed. There was a nice patio for spending time outdoors. It was nice to sit out there and chat with other travelers.
In Siena we stayed at a fantastic Agriturismo. If anyone would like more information about it I would be happy to share via Private Message.