I was in Uganda in March and April this year, returning in Jan. thru March. I do malaria education work in the villages. I prefer to fly Emirates as the flight from JFK is usually only 1/2 full with 13 stewards and stewardess to take care of you. Plus you get 8 hours in Dubai to look around or visit the gold souk. I'm going KLM this Jan due to schedules.
I stay at the Boma Inn at EBB. Its used by the UN pilots out of the Congo.
Run by a great young couple. Her name is Seija, a Finn from Tanzania and SA. Its like the 30's out of Hemmingway.
My base is Bujagili Falls 7 clicks from Jinja at the Nile River Explorers Campground. You can get gorilla permits for $325 a person which are needed. You will get within 5 to 10 feet from a silverback so have a camera and be ready to be awed.
Rwanda is beautiful, very French with clipped lawns, boda drivers with colored vests and helmets (most of them anyway) Much safer than riding in Uganda. PS don't ride at night.
If you can go to Bujagili Falls on the Nile and stay in a dorm, 2 bunk beds for $5, a banda for $20 or at the Nile Porch with great accomodations for $54 including a pool. It overlooks the Nile and provides the worlds best 30 KM of class 2 to V rapids for kayaking and rafting. Most of the top raft guides in the world come here and all of the top kayakers have been or are here. An all day trip is $95 with an extra $45 for a professional DVD of your trip and spills.
Hope this helps, have a Nile Special beer while there.
Tom