Turkey has an extensive system of intercity buses for travel around the country, and Istanbul's large, chaotic Esenler Otogar is the heart of it. Esenler itself is a bit out of the way, though easily accessible by metro from Aksaray and many of the bus companies have offices around the city and shuttle buses, known as a "servis," that collect passengers from the city and take them to their own mini-bus stations on the main freeway, allowing you to avoid the otogar completely.
A second smaller bus station, on the water on the Asian side of the Bosphorus, at Harem, is easily accessible by the car ferries from Eminönü.