Java iButton on PocketPC
Initially you need a working Java comm api install, if you follow my 'Java COMM API Support on the PocketPC' you can just add OneWireAPI.jar to the classpath - though there seems to be some constraint on the length of the registry key for executing pjava.exe, and if it is too long you'll just get an error when you try to run a .class file.
If you are trying to use the iButton OneWireAPI with the CEJavaComm the code has to be modified & recompiled so that it doesn't try to change the parameters of the com port. From memory, the file you need to change is USerialAdapter.java, though I'm not 100% sure. My modified version is here it contains the modified and compiled source, and also has the debug variable set one some of the classes (and probably some other debug output that I found useful). If you want to capture System.out & System.err remeber you can redirect them to a file.
If you are using CrEme 3.2 the original OneWireAPI can be used.
Once you have go your comm api & classpath setup and working you need to run the SetDefault app from the samples directory of the OneWire stuff, to choose the port, adapter type & check it's working. I've modified the original version to use awt instead of the console (as I couldn't get System.in work properly CrEme), and it's here. If you have any problems it's most likely you classpath will be wrong or your files will be in the wrong places. The adapters I have working are the DS9097U's, and the external comm port always seems to be COM1.
Good luck!