will let you choose flights to track and send you email alerts of price changes. You can even set alert prices. It's free to set up an account. I've had good luck using it.
Published fares are usually lowest on Tuesdays for whichever days you decide to travel, but generally speaking it's cheaper to fly midweek(Tu,We,Th) if you can.
Most travel sites- I prefer Orbitz for it's ease of use- will give you a 3 days grid for comparison. Then I book directly with the airline.
If you're going to be flying on a regular(or even occasional) basis it is to your advantage to pick an airline with good service at your home airport, set up a frequent flier account, and stick with them as much as possible. Miles add up! I've gotten free/reduced fare flights just using miles over the years, and I only make two or three trips a year.