Vinegar is the secret ingredient of Carolina Barbecue, particularly apple cider vinegar. 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 anytime 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 vinegar. North Carolina is divided on the issue of sauce. 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. 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 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 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
Now, like any other barbecue sauce it is best made in advance. You want to give the flavors time to mix. The vinegar will literally dissolve most anything you add to it. 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.