I assume you mean difference between the scripts in /etc/init.d/ and /etc/rcX.d (and not /etc/init.d/rcX.d) where X is the runlevel.
The scripts are located in /etc/init.d/ and not in /etc/rcX.d. In /etc/rcX.d there are only links to the scripts in /etc/init.d/. If you run:
for example you'll see what I mean. The only difference is that the links in /etc/rc2.d are proceeded with a letter S (for start) or K (for kill) and a sequence number so an administrator can indicate the run order of the scripts when entering a specific run level.
Hope that helps.