JIRA is indeed one of the best issue tracker in the market. The best thing about this tool which I like is the customizations that you can do in it that too managed from the UI itself. Of course there are lot of things are can be done through the interface but sometimes there could be a possibility that you are looking to implement some behavior in the the interface but couldn't find the right solution.
JIRA comes with an in built feature to change the colors of various elements, you can also upload your own logo on top and use the colors that are standard in your organization. Though sometimes changing the colors might not be sufficient. You may want to change the size of regions, or giving extra padding at certain locations. How would you do that. There are certain add-ons that you can use to install various theme that can change the look and feel completely but I prefer to have my own style.
It is possible to insert your own CSS file and override the default look and feel.
If you have been working on Drupal creating websites then I am sure you must had a need to clone or duplicate a node. Let me give you an example. These days I am working on a website for one of my client where we need to display electronic house hold products like Water Heaters, Ventilation Fans, Cooks Tops etc. Now most of these products in the same category have similar attributes but only difference in size or color. Now when we add a new product it is a pain to fill all the fields that contains the product specifications. I thought there must be a way to clone it.
Here is another small tip for designing drupal website. When you develop sites in drupal you be definitely need to modify the existing css file of the theme you are using. my suggestion is don't mess much with the original theme. Keep it as it is or change it only when you really have to.
Just create your own css file, lets say we call it MyOwn.css and write your code in it. Then edit the .info file of the theme you are using and add the following line in it.
stylesheets[all] = style.css
stylesheets[all] = ribbon.css
stylesheets[all] = aggregator.css