Muhammad (PBUH) used to recite Du’aa al-Qunoot during Witr prayer (as well as during Fajr prayer and at other times throughout the year).

There are a few different forms of du’aa al-Qunoot. Here are a couple:

This recitation (along with the transliteration and translation), is recited during Witr prayer by those of the Hanafi madhab:

This recitation by Mishary Rashid Al Affasy (along with the Arabic text, transliteration and translation) is recited during Witr prayer by those of the Shafi’i madhab.