I have been using Mint.com for a while now. But one thing always scare me, that one day free version would go away, or even Mint.com would shutdown. Then we will have to find a new replacement.
Luckily, Mint.com provides csv export of all transactions with categories and labels. This way I can make my local backups and if need be, hopefully, these transactions could be imported into whatever comes along. Also csv export let me do my own analysis in Excel and Google spreadsheets.
Now I have also started to use git to track changes in csv exports. Just in case some old data changes, git would display diff easily. Before I was keeping multiple copies and csv file, now I have just one file in git repository.