Entering through Entebbe airport

You can pay USD$50 to get a visa from the Ugandan embassy in Washington DC which requires that you mail your passport or you can show up at the airport with USD$30 (if you give them euros they still ask for 30 which of course is waaay more expensive) and you buy your visa there. If you dont want to wait in the long line with everyone else who is getting their visa at the airport then you can spend the extra USD$50 + shipping and go in the COMESA (African org) line and get processed very quickly.

(Update: getting a visa at the entebbe airport is USD$50 now)

Entering overland

From Kenya - stock up with fuel in Kenya as it is more expensive in Uganda. The Malaba border crossing is the main one and is consequently the busiest and attracts the most hassle. The Busia crossing is not far away and somewhat quieter. Avoid the crossing to the north of Mount Elgon (on the way to Sipi Falls) in the wet season as the road can be atrocious. 

You don't need the help of a 'clearance agent' or helper to get through, it's all reasonably straightforward. At immigration, you can buy a visa on the border for US$30. At customs, if you are bringing a vehicle in you have to pay 36,500 Ugandan Shillings (about US$22) for road tax for 14 days. You can only pay in shillings so you will have to use the moneychangers, unfortunately. There was a 2,000 shilling 'bank fee' on top of this which is probably a scam but probably not worth arguing about.  If you have a 'Yellow Card' insurance certificate you won't need to buy car insurance at the border. Don't try and cross with a vehicle without a Carnet, it will cost you hundreds of US$ in fees and bribes.