Vinegar is the secret ingredient of Carolina Barbecue, particularly apple cider vinegar. In this region that tangy flavor is what makes for great barbecue. Straight cider vinegar is used as a marinade, before cooking, as a baste during cooking and as the primary ingredients of a finishing sauce served on barbecue at the table. The secret of using vinegar with barbecue is to give it time to work it's way into the meat so that you won't be left with a strong bitter flavor. You need to balance the sweet flavor of slow cooked meat with the flavor of the vinegar. The advantage to vinegar barbecue sauces is that you can add them in at any time and the vinegar easily works into the meat. This allows you to add spices and have them sink into the meat giving it plenty of flavor.
Of course, there is more to a good vinegar barbecue sauce than just the vinegar. North Carolina is divided on the issue of these types of sauces. On the eastern side, vinegar is kept pure, particularly of those nasty tomatoes. However on the west side, barbecue sauces are put together with a hint of tomato and sugar, which balances the flavor with a hint of sweet. Now while the purists will keep to these formulas others have taken to the additions of cayenne, brown sugar, molasses, red pepper, red pepper flakes, etc.. These thin sauces can come in so many different variations that they could challenge the thick, sweet sauces in variety.
The vinegar used for this style of sauce is usually apple cider vinegar, but plain white vinegar works as well. In fact, any vinegar will work provided that the other ingredients match the flavors. Try balsamic or fruit-based vinegars. The advantage of vinegar in sauces is that it has an additional tenderizing effect that helps make barbecue pull apart perfect. The gentle acid of vinegar tenderizes the meat during the process making it as tender as possible as well as adding that tangy flavor that is the cornerstone of Carolina barbecue.
Now, like any other barbecue sauce, vinegar sauces are best made in advance. You want to give the flavors time to mix and combine over time. The vinegar will literally dissolve most anything you add to it and giving it a day or two to work its magic makes for a far better sauce. If you add coarse ingredients like red pepper flakes you really need to give it a day or two to pull the flavors out into the vinegar. Also, vinegar-based barbecue sauces have a long shelf life provided that they are stored in the refrigerator. It is good to make these sauces in large amounts to keep on hand.