I have been using Mint to manage my finances since April of this year and I love them! They are run by Fool.com. It is completely free and safe (please read all of the safety features yourself).
Basically, you can see ALL of your accounts using mint. Your credit cards, checking accounts, savings accounts, mortgage, etc. Everything updates to the minute when you log on. Mint classifies all of your purchases (if they are on a credit card or came out of your checking account) for you and puts it in a nice graph that shows how much you are spending on what. If you take cash out of your savings account you can break that down by purchases so it will also be included. The only thing that can’t be included is cash that never touched an account.
They recently added an investment section that tells you how your investments are doing at one glance. It gives you the price you paid for them, what they are worth, and the percent difference.
I highly recommend this site for anybody who is trying to stay on a budget!