A great feature within Guild Wars goes unnoticed by most. You can organize your templates in folders!
There are 2 ways to accomplish this.
While in game, typing "folderName/templateName" into the template name. The slash (/) will tell the game to create the folder. Of course, you could also do something like: folderName/subFolderName/templateName. This would allow you to create folders and sub folders.
When outside of the game, you have to find the Template folder on your computer and create the directories (aka: folders) that you wish to use.
In Vista: C:\Users\(your user name here)\Documents\Guild Wars\Templates\Skills
In XP: C:\Program Files\Guild Wars\Templates\Skills
You cannot remove or organize folders through the game interface.