Prophet's Supplications In Meezan Book
Meezan is book for comprehensive introduction to Islam. If I remember correctly, there are no prophet duas specially mentioned. For istikhara you can chk this thread Discussion 38684
In addition to Duas mentioned by Faisal Sahab, You can also find additional duas in Meezan Chapter “Morals and Morality” under heading “Pinnacle of Morality” under subheading ” Remembering God in abundance”