Search other flight sites. After you find your best fare, set up a flexible airfare calendar on the ITA Matrix. (search on different search engines: google flights, google, bing, firefox, safari, etc.)
Apply for fare alerts on these sites that will tell you when and if the fare goes down.
Choose 2 to 3 airports to fly from and to if possible.
Breaking up your flight with different airlines will sometimes save you money. Regional aircraft on short flights are usually cheaper (especially Internationally).
Use one credit card for all miles. Claunch uses Capital One.
Apply for a few different frequent flyer miles accounts. i.e. Capital One, Delta, Alaska Airlines, etc. Combine miles from partner airlines if possible.
Claunch calls 3 airlines that he has miles with and asks the booking agent for help.
Once you book, you have 22 hours to change your flight, so continue to watch your Fare Alerts.
Sign up for TSA Pre-Check to make going through security easier.
Sign up for Global Entry to forego immigration on International trips.
Book your car rental and hotels at the same time to save money when you add them.