I use Excel and Mint.com. Once or twice a week I download transactions from my online accounts (Chase and AMEX) to the excel sheet. I type in my checking account balance then subtract my credit card balance and any bills I need to pay. If I have any reimbursable expenses for work I separate these out. This way I can make sure I'm not spending more than I have and can pay off the cards in full every month In the excel sheet I also track the date I applied for cards, the bonus categories, and annual fee amount.

I use Mint.com to see how much I'm spending in each category and try to stay on budget.