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system
what headaches will i have switching from quicken to gnucash?
user
i have not used quicken; i've used gnucash exclusively.  it feels a bit rough with the ui: balancing that, the data is stored in a gzip-compressed xml file. the compression is also optional, so you can save it as a plain xml file.  this means that you have some hope of recovery if you wind up with a corrupted file. (and for programmer-types, you could keep it in source control for additional peace of mind.) my wife and i have been using it for several years now, and has worked well for us. lwn.net had a pair of grumpy editor reviews on personal finance software here and here which would be worth reading.
assistant