The Last King of Scotland by Giles Foden. A gripping novel told through the eyes of a fictional Scottish doctor who becomes personal physician to Idi Amin. It captures the paranoia and violence of Amin's regime while painting a vivid picture of 1970s Uganda. The film adaptation with Forest Whitaker is excellent too, but the book goes deeper.
The Abyssinian Chronicles by Moses Isegawa. An epic novel that follows a Ugandan family from the final years of British colonialism through Amin's terror and Obote's second reign. Isegawa writes with fierce energy about the chaos of post-independence Uganda. Not an easy read, but a rewarding one.
Uganda: The Bradt Travel Guide by Philip Briggs. The most detailed and reliable guidebook dedicated to Uganda. Briggs has been writing about East Africa for decades and knows the country intimately. Essential if you are planning an independent trip.
The Gorilla Highlands by various contributors. A community-driven guide to the southwestern corner of Uganda -- the gorilla tracking region around Bwindi, Lake Bunyonyi, and Kisoro. Available free online. Excellent for cultural context and off-the-beaten-track suggestions in a region most visitors rush through.
A Grain of Wheat by Ngugi wa Thiong'o. While set in Kenya rather than Uganda, this novel about the Mau Mau uprising illuminates the colonial dynamics that shaped all of East Africa. Short, powerful, and essential reading for understanding the region.
The Wizard of the Crow by Ngugi wa Thiong'o. A wildly satirical novel about a fictional East African dictatorship that draws on the absurdities of real post-independence politics. Funny and furious in equal measure.