If your under Kanotix (which is afaik a Linux), why do you want to start it with the parameters "C:\>java" and "C:\Dokumente und Einstellungen\pooky\Lokale Einstellungen\Temp\mole-4.41\mole-4.41.jar" ?
Also your command
java -jar "C:\>java -jar "C:\Dokumente und Einstellungen\pooky\Lokale Einstellungen\Temp\mole-4.41\mole-4.41.jar"
can't even work in bash or another shell, 'cause the quoting is wrong!
What would be a possible input to this program and what means "[ghqALRV]"?
The [] says, you can optionally choose on this position between those parameters or leave them out. so any of the -g and so on, can be used here. Look in the list what they mean. The only parameter needed here is <file>, where you have to put your filename (of course, without the <>).
How do I have to write an input to the command window ( e.g one of the options)?
rtfm: man mole or info mole. or google for it.
If your problems concern specialties about the mole-program (which I have no idea what it does), you probably should search the net or ask people on irc, or look for contact on the home page of the mole program.
vielleicht solltest du nochmal auf deine Versionsnummer schaun (ich glaube du meinst FC5).