The most famous Malay Sultanate was from Malacca Empire History... During that time, Sultan played major roles in ruling the government.
Nowadays, the sultans still have strong influence in malay community in Malaysia. The Monarchy System nowadays, acknowledge the Yang Di-Pertuan Agong as the head of the country. Malaysia practices a system of government based on Constitutional Monarchy and Parliamentary Democracy.
At the Federal level the head of State is the King and the head of government is the Prime Minister. At the state level the head (Ruler) of State is either the Sultan, Raja, or Yang di-Pertuan Besar, and the Yang di-Pertua Negeri is the head of State where there are no Rulers: the Chief Ministers (Menteri Besar/Ketua Menteri) are the heads of government.

CONFERENCE OF RULERS
In accordance with the Malaysian Constitution, the power to elect and appoint the Yang di-Pertuan Agong is vested with the Conference of Rulers. In the federation system of government (as practiced in Malaysia) where a number of state Rulers are involved, a council known as the Conference of Rulers, was instituted under Article 38 of the Federal Constitution to serve as a forum for the Rulers and Governors (Yang Dipertua Negeri) to meet and deliberate. On certain matters the Federal Constitution provides that the government seek advice from the Conference of Rulers.
refer to: http://www.malaysianmonarchy.org.my/portal_bi/rk1/rk1.htm