Oh, and the reason I chose Quark was more about budget than anything else. Their reputation was sufficiently good, and they didn't have a lot of extras, so they seemed like the best bang for the buck. It was a great trip - one of the best I've ever taken.
The big budget operator is GAP - they bought one of Lindblad's old ships, but their itineraries were too short. Given that you spend 2 days getting to Antarctica and then 2 days going back, I wanted to get as much time out there as I could afford. So, that's why I didn't consider them.
Lindblad seems pricey, but if you look at everything they include, they compare pretty well. They tend to stay at upscale hotels and include transportation and whatnot, so it does drive the price up if you want to economize. Cheeseman's is pretty pricey, as well, but that's because their trips are so long. Their per day costs aren't bad.
In terms of picking a cruise, I used the following criteria:
Itinerary - Just the peninsula or South Georgia and the Falklands, too? Not everybody does the longer trip, so that may eliminate some contenders.
Length - as noted, figure 4 days used going to and from antarctica. So, look at how many days you actually get in Antarctica doing landings and figure your per day costs for any given itinerary.
Ship - I wouldn't do the trip with a ship bigger than 100 passengers. Takes too long to get everybody out onshore, and for the really big ships, you have to do your landings in shifts. Some ships are nicer than others. Lindblad's ships are definitely very nice - gyms, spa services, e-mail stations, etc. Quark's are a bit utilitarian, but comfortable - they are converted research vessels, after all. But, really, you're either going to spend your time wedged in your bunk riding out the Drake Passage, running around in Antarctica, or in your cabin exhausted from all the running around - and, even then, you'll probably want to spend time up on the bridge watching icebergs go by.
Quality of Guides - you'll have to figure this out by reputation, but as noted Lindblad and Cheeseman's have great guides. The guides I had on Quark were very good in my estimation. I've talked to people who have done Peregrine, and they were quite happy as well.
Special Interest - If you have special interests like kayaking, climbing, or photography - certain cruises are going to be more geared towards what you want. My cruise was a general cruise, and if I had to do it over, I would probably have picked a photo-oriented cruise since that's where my interests lie. Quark tends to do general cruises, while Lindblad, Peregrine, Cheeseman's, etc... will have specialized cruises - perhaps have historians onboard to talk about Shackleton's voyage, or professional photographers to help guide your photography.
Extras - make sure to calculate what's included so that you're comparing apples to apples in choosing an operator. As noted, Lindblad usually has upscale accommodations included in their packages. They're also very well organized, so you'll never have to worry about anything, and they'll take care of you from end to end. For my Quark expedition I was pretty much on my own until I showed up at the hotel in Ushuaia, and was on my own again once I got off. Some cruises give you the bright red parkas and rubber boots. Some expect you to bring your own gear. Some include things like alcohol, others charge extra (a lot extra). I think everybody charges for laundry.
I'm an independent traveler by nature, so Quark worked out well for me. I made my own arrangements, brought my own gear, and used the savings to afford the length of trip I wanted. I enjoy nice facilities, but I was also completely satisfied with what I got from Quark.
However, when I go back (not "if), I'm doing South Georgia and the Falklands and it's going to be a photo-oriented tour. But, those are my choices - I just have to save my pennies to afford it.