There are some bagels and other grain products masquerading as whole-grain or whole wheat. Marketing gurus are quite clever in disguising what's really in their products. Just because it's brown doesn't mean it's whole-wheat or whole-grain. Some products contain caramel coloring to give it that brown whole-wheat/grain look. Also, steer clear of products using phrases such as "wheat", "enriched wheat flour", "multigrain", "5-grain", "rye", "made with whole wheat", "made with whole grain", or "contains the goodness of whole grain." Unless it says 100% whole grain or 100% whole wheat, it's probably not. Check the ingredients on the label. The closer to the front of the list the more it contains. Look for breads that have at least 3 grams of fiber. If you're at your local bagel shop or bakery, ask them to tell you about their whole-grain and whole-wheat products. In my experience they're more than willing to share with you what goes into their various offerings.
Also, you need to know that there are some differences between whole wheat and whole grain. Both are good for you and both are much better for you than processed white flour. The biggest difference between whole wheat and whole grain is the process used to prepare the grain flour. 100% whole grains are made from the whole kernels of grain (both the inside part of the grain and the outer covering). If a product says "whole-grain," that means the grain flour used to make the product has not been refined. A benefit of it not being refined is that it takes longer for whole-grains to digest. Because of this, it has a glycemic index of 50 which is fairly low. 100% whole wheat does in fact mean the whole wheat kernel is used, but that doesn't necessarily mean it's 100% whole-grain flour because often the whole-wheat has been refined to give it a lighter texture. When the grain has been refined it's striped of some of its nutrients. Because 100% whole wheat is often refined it's digested more quickly, giving it a higher glycemic index (around 71). So, if you have trouble with spiking blood sugar, eating 100% whole-grain is a better choice. Visually it's hard to tell whole-wheat products from whole-grain. Whole-grain products usually have a richer, heartier taste and involve more chewing when you eat them. Both whole-wheat and whole-grain products are much healthier for you than refined and bleached flour products.
Active people, especially runners, need a good healthy diet that consists of about 50% carbohydrates, 20% protein, and 30% fat. But you have to be careful not only with the percentages of carbs you eat, but also the kinds of carbs you eat. Like with most things, there's good (complex carbs) and there's bad (simple carbs). Only 10% of your daily carb intake should be of the simple variety (sugar, honey, white bread, GU, and refined foods like cakes and cookies). The other 40% should be comprised of complex carbs. Carbs convert to glucose in the body which is used for energy or stored in the muscles or liver as glycogen for later use as energy. Carbs become the bad guy when you're not active. Only a limited amount of glucose can be stored. If there's "extra" in the body that's not being used for energy, it becomes stored as fat. Runners use carbs as fuel. Unless you're over indulging and not running, you shouldn't be worried about weight gain.
Whole-grain breads are a good source of complex carbohydrates. They have as much carbohydrates as whole-wheat or even bleached-flour products, but whole-grain products are absorbed into your system with greater ease and tend not to create as much of a spike in blood glucose levels as the other types of breads. Also, for all the "I'm going to gain weight" sayers, whole-grain breads are a good source of fiber and a diet with sufficient fiber can help make you feel full longer which can help with weight loss. Whole grains can also help to lower cholesterol.
So runners, take heed! Eat that bagel (whole-grain that is) and be proud!