Long gone are the days when people use tomboy notes or gedit files to store passwords (not true, i still see such people around me on daily basis), now they use KeePassX. Its a very nice and handy tool, best thing about it is that its Cross Platform. I have been using it since years and i never found any issues with it.
You can install it on ubuntu/debian like:
apt-get install keepassx
For other platforms, visit this link.