The chuck is the best for pot roast. It's what they call the shoulder for beef. There are many different cuts that will work. Some are boneless, some are bone-in. Unless you're cubing it for chili or stew, bone-in is more better. Chuck has lots of flavor, but it's too tough for most cooking methods. The pot roast/braise method is good for chuck. 3-4 lbs is a good size.

For the liquid, store-bought stock is okay. Stock made by a butcher shop is definitely a step up. Adding some bold red wine is good. You want to be on the Cabernet, Zinfandel end of the scale. You want the liquid covering 1/2. One major role of the liquid is to control temperature. While the oven may be 350, the interior of the dutch oven is kept much lower due to the liquid.

The recipe of the interwebs is endorsed by Cynthia and me, with some mods.

http://www.foodnetwork.com/recipes/fancy-yankee-pot-roast-recipe.html

- Use chuck, not round. Dredging is optional.

- Saute the onions, take them out, turn up heat and then brown the meat. Onions and a 4 lb hunk of beef have different browning requirements. A pan hot enough to give the beef a nice sear is going to burn the crap out of the onions.

- Add some bay leaf along side the thyme.

- You don't need to make gravy. You can just reduce the braising liquid to make a sauce. The onions will have fallen apart by then, and will give it some body.

- As Steve mentioned, there are other veggies that can work in this. There are different ways to handle the different cook times. This recipe calls for pulling veggies out of the pot when done. Some people cook the veggies in the liquid after the meat is done. Or, you can add veggies after the meat has been cooking for a while.