I just purchased some nice beef marrow bones. What I'd like to do is make myself some beef stock for soups and whatever else. Now I'm planning on making a Mirepoix and then adding the bones and then the water. However, my question is this: do I just put the bones in how they are or do I cook them in the oven?
Both methods are acceptable.
A stock made with roasted bones is called a brown stock. A stock made from raw bones is a white stock (or sometimes just stock).
Practically, it's very difficult to get a true "white" stock with beef, as opposed to chicken, since all of the impurities will darken or cloud the colour - but that is semantics.
Brown stocks have a richer flavour, but that does not automatically make them better - it depends on what you'll be using it for. For soups, where the stock will give most of the flavour, brown is generally preferred; however, as a "flavourful liquid" to use in sauces, risottos, etc., a white stock may be more useful because you don't want it to overwhelm the other flavours.
One cautionary note: Beef bones tend to give off a lot of what looks like blood (actually myoglobin) when boiled. If you're trying to achieve a perfect clear stock (white or brown), then you may want to blanch them first; dump them in the pot, bring the water just to a boil, then dump out everything and start over. You really won't lose much; most of the proteins are deeper within the bones and requires several hours of simmering to extract and denature.
If making a brown stock (from roasted bones), do this after roasting, not before. It will also help you to get rid of any excess oil so you won't need to skim as much.
Before you make a beef stock, rub down the bones with tomato paste, then put your mirepoix on top, then roast your bones at 450 degrees for 30 minutes. Let the stock simmer for 24 hours. Beef stock simmers for a day, chicken stock for about 8 hours or so, fish stock for an hour.
Another option for beef stock, since the bones need to cook so long, is to cook the bones for several hours before adding the mirepoix. This allows the stock to gain a stronger beef flavor before you add the other seasoning.
One warning though -- stock does best if it cooks at a temperature that's barely a simmer -- a bubble or two every so often. According to this question, a simmer is about 180 F -- significantly lower than the 212 F of boiling.
All the answers above are all correct. I find that after you roast your bones , I then add my mirepoix with whole garlic and herbs. Once colored up, add tomato paste cook until darkens. Remove and deglaze pan with red wine , scraping the bottom to remove all the flavour. I think beef is 8-10 hours, chicken is 3-4 hours and fish is 20 mins once come to the boil( skimmed and turned down).