I just wanted to say that I used the tour operator Patagonia-Argentina, and they were very helpful and the entire trip went off without a hitch. I would highly recommend this tour operator when planning a trip to Patagonia.
http://www.patagonia-argentina.com/i/

My wife and I were on the Mare Australis tour from Ushuaia to Punta Arenas this past February. We had a great time and I highly recommend it. I'll try to answer some questions that I had before I left.
First, you check in after 9:00 AM at the Cruceros Australis office in the center of Ushuaia. They take your luggage, provide you with documentation, and send you off to await boarding at 5 to 6 PM. We had about 8 hours to explore the city. Frankly, there's not a lot to do in Ushuaia, and you could probably use a full day here to explore the areas outside of the city. We took a city bus tour ((not much, but someting to do), visited one of the small museums, walked a lot and shopped a little. The weather was variable and changeable. Layers and waterproof treking shoes are the best idea for this region. We had lunch at Tante Nina (good) and went to the pier at 4:30 to await boarding. The pier is down at the harbor, but it's only 5 minutes (down a hill) from the center.We were able to board at 5:30, and we were brought to our cabin by one of the staff. We were on deck 4, and the cabin was nice. The ship is small (120 passangers) and it's easy to get around her. Decks 3 and 4 each have a bar/reading room/observation lounge and are a short walk from the cabins on those decks. These rooms are also used for the daily orientation programs that go over tours available the following day. Meals are offered on the dining room on deck 1. We had a table set for 10. Meals were fine- not haute cuisine, but good and served by a congenial and efficient staff. All drinks were included. The wines were fine. I didn't expect nor did I receive Achaval Ferrer, but the wines were varied and good. It was on the expeditions that the ship was able to really shine. We landed on and then circled on the outside of Cape Horn, visited a nature sanctuary, approached glaciers through a field of broken ice, observed condors in their nests, and landed on Magdalena Island and observed the penguins up close . The size of the ship and the use of the Zodiacs made the tours spectacular. As we arrived in Punta Arenas and disembarked, we were able to get a taxi to the airport for $20 US and begin our journey home. BTW, since we were leaving Chile, we didn't have to pay the $100 visa fee.