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.