Make sure you're using Ziploc specifically -- as in that brand. Other manufacturers may have their own formulations for their plastics, including non-heat-stable plasticizers. I contacted Trader Joes, for example, when writing Cooking for Geeks, and they disclosed that their plastics are NOT heat safe.
http://www.amazon.com/Lekue-1-Liter-Fresh-Bag-Clear/dp/B0049...
In theory you can use anything that handles the temperature, such as silicone. You could in theory force your food into a jar with a bit of oil.
- It makes the size more manageable in your water bath. - You don't have to worry as much about temperature ramp-up time between outer surface and core of food item. - For delicate proteins, means there's less handling of the item post-cooking.
-Jeff
I still use bags most of the time, because I don't think running a cooker at 55 deg C with bags rated for 90 deg C is going to be an issue.