What are the benefits of choosing either:
~/.myapp/configI already know a couple of things; storing data in the user's gconf database makes it a little harder for the user to copy those settings out and onto another account or computer. On the other hand, is it true that using gconf would be easier as the underlying data storage facilities are already sorted out, without you having to write your own configuration file handler?
I'd go with GConf.
However...
Perhaps if you are worried about users copying their settings in and out of the program, you should create import and export settings functions into your program? A user could then potentially save those settings in cloud storage like Ubuntu One or Dropbox and simply import their desired settings into GConf using the utility that you provide, regardless of the machine (even if they prefer to run from liveCD). Either way, very clearly indicate to the user where the settings are being stored. Many (but not all) Ubuntu users are comfortable backing up and restoring those configuration files by themselves using rsync or another backup utility.