The thought of entering the Congo is enough to give most people the heebie jeebies. While it is anything but simple to do, it is possible to do with a little patience. I crossed into the Congo in mid-November 2008 at the Kasindi border with the help of an interpreter from Go Congo.
To enter at Kasindi, you must first make your way from the main Fort Portal-Mbarara road to the border. Kalita runs buses from Kampala to the border. Alternatively, you can hire a local car to take you to the border from the intersection where the road to the border meets the main Fort Portal-Mbarara road. This costs $5-$10, however you can pay the same price from Mbarara to the border on a Kalita bus.
Once at the border, you must fill out an exit form in the Uganda border office (left side of road). This is generally straightforward and painless. After this, your local car, or motorbike, can take you the next few hundred meters on the zig-zagging, rough road to the Congo side. Alternatively, you can walk this.
Immediately after crossing the border, agents will know you are a foreigner and will take you inside a very small office. Here, you will be asked to empty your bag(s), and they will do a thorough search of everything. Luckily, I was able to get through this without them confiscating my satellite phone nor camera. When they're done, they ask for a bribe (or drink)...just play dumb, ignore them, and leave.
Now, you enter the main border office to get your temporary visa/permit to be in the Congo. On the temporary permit, they will list your itinerary. To avoid future hassle, be honest and tell them your itinerary. I was with an interpreter from Go Congo, who knew a high ranking border official. Still, we waited over 45 minutes before we finally got the permit (an 8x10 sheet of paper). A 7 or 8 day permit costs $50, plus a supposed extra $10 for them to stamp your passport. Once this is done, you are free to leave their office, though they will ask for a bribe or drink (again, play dumb and leave ASAP).
If you plan on staying more than the permit allows, you MUST renew the permit and pay another $50-60. This can be done in Beni.
After getting your permit, you then must walk next door to where they check your yellow fever vaccination certificate. This supposedly costs $2, though I suspect the $2 I paid was another bribe. Once this is done, you're all set and free to go further in the Congo. Just keep the permit with you at all times, as it will be scutinized often from this point forward.
To avoid some of the hassle at the border, obtain an official visa prior to arriving at the border.
P.S. Do not take photos of anything in the border area.