A couple of things about the sample label editor. First of all, after the user loads more than 8 or so samples, the JTable holding the sample information is too wide for the screen and needs to be put in a scrollpane. Scrolling horizontally like this is a pain in the neck, especially if you are trying to move samples from one side of the display to another. I think it might be a good idea to display the sample data in a vertical format, so it will fit better.
Secondly, I think sample reordering should be enabled by default. This is addressed in a bug report. (http://sourceforge.net/tracker/index.php?func=detail&aid=1669475&group_id=110558&atid=656691)
Third, I think some auto-sorting functions for the samples would be very useful. It would be nice if there was a button on the editor that allowed the user to sort the samples alphabetically by an annotation field, for example.