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Many thermal jackets or other athletic jackets have hoods to keep your head and ears warm and dry, so seek out a hooded style if you know that you'll often be working out in cold, wet weather. For versatility, some styles of fitness jackets have detachable hoods, or hoods that stow away into the jacket collar when you don't need them. Some hoods are simply a light shell of material for rain resistance, and others have some type of lining for warmth as well.
If hoods really annoy you, combat the cold with a sports hat. Close-fitting beanie-style hats are ideal for cold weather, and most sports apparel manufacturers offer hats in thin, moisture-wicking fabrics or heavier fleece fabric. The disadvantage of cold-weather thermal hats is that they don't always cover your earlobes. When it's cold, I feel colder if any part of my ear is exposed. If you feel the same way, opt for a lightweight fleece earband instead of a hat.
A bonus layering tip: If it's really cold/windy/rainy, wear a light moisture-wicking beanie (or an earband) underneath the hood of your sports jacket and you'll be ready to brave any elements.