Chris Blattman recently posted an excellent reading list on northern Uganda. I particularly recommend Alice Lakwena and the Holy Spirits (Kampalans: you can get this at Aristoc) and the reports published online by Survey of War Affected Youth.
Trial Justice gave me a much better understanding of the International Criminal Court’s role in the conflict, and I’ve been glued to the Uganda Conflict Action Network blog since it began in the summer of 2005.