Okay, this is offered with the usual disclaimer of it's how I did it and if you hurt yourself, don't come back after me!
First, you are smart to be concerned with any quick cleaning causing chunks to go into the engine. I've seen it happen. No major damage, but stuff that needed to be fixed.
Now, the passages are almost always rough walled, twisted and the diameter varies. In other words, they are not easy to clean. any method except the last one will leave some stuff behind, and you want to make sure it is not going to fall off on the first drive.
The first method is cleaning fluids. This works only mildly and is only useful if the passage is clear and you are just keeping the deposits from building. This can be done without removing stuff at both ends, since it's not going to be getting big chunks loose. Make sure you don't allow a lot of fluid into the engine.
Second is to remove the valve and anything in the way of the other end of the passage. Fluids again, along with any tools, brushes, coat hangers or speedo cables will fit into the passage. You want to catch all stuff that gets dislodged so it doesn't go into the engine. Compressed air is important here. Blow back toward the valve!
Third is the second, taken to a higher level with the cleaning bit on the end of the speedo cable.
Here's the tool (warning! flash and sound!)
http://www.califautotech.com/snake-bit.swf This will work in a lot of cases, but expect the tool to be expendable, and they are not cheap!
Last method. I caution you on this, since it does require flame. Have a helper and fire extinguisher nearby, make darn sure you know what you are doing, and think and plan ahead to avoid bad things. Oaky, for the really plugged passages that are cast into the manifold with all sorts of twists, this method provides great results. It gets them really clean. First, remove everything near each end for access. Also make sure all flammable stuff is moved aside and there is no fuel nearby. Blow compressed air into the area and the intake to remove any fumes. Fire up your oxy/acetylene torch, preferably a small tip. Point it at the EGR end of the passage and get the deposits burning. Now, turn off the acetylene, so only the oxygen is coming out of the torch. This will cause the coal-like deposits to burn like charcoal and clear out the entire passage. It is also dangerous, so make sure you understand what you are doing and what are the possible issues that can happen. You might even want to take the intake manifold off the vehicle before attempting this. Clean carefully after and reassemble.
