Without a doubt the best tool and system out there is You Need a Budget (YNAB, for short). See this website:
http://www.youneedabudget.com/
This tool and the thought behind it blows Mint.com or spreadsheet budgeting out of the water. Trust me. It has a cult-like following because it works so amazingly well. You think about money in a completely different way (category balance vs. bank balance).
Over the past couple of years it has completely changed my life financially. It takes a little bit of work - but the payoff is so well worth it.