I've tried a lot of different ways to track my finances (Excel, MS Money, Mint.com, creating my own website) but I think the best one is a spreadsheet within Google Docs.
Google Docs is good because it's free, Google won't lose your data, you can access it from any computer, you can make nice graphs, and you can set things up however you want to.
A couple of people have asked me how I made the graphs in my journal, so I cleaned up my personal finances spreadsheet and removed all the personal data. You can access that here: ERE Finances
Fair warning: it's not the most straightforward of spreadsheets. Let me know if you're confused by anything.
You can use this to make graphs like:
(check out the Graphs sheet/tab on the bottom of the spreadsheet)
I hope you find this useful! Let me know if you do anything cool with it. (Start by doing File -> Make a Copy)