When you say "system variables", do you mean system environment variables?
If so, the FastCGI processes will inherit the environment variables from the worker process in which they are launched. IIS 6 does not have any built-in facility to provide custom environment variables for worker processes. It is pretty trivial, though, to write an ISAPI filter that can do this job. If this is what you need, then let me know and I can set you up with some sample code to do it.
Also, I should note that IIS 7 does have a built-in facility for doing this. Specifically, IIS 7 can load the user profile into worker processes. Thus, different app pools can use different user identities, each getting their own set of environment variables.
Finally, I was just talking to Rick about the issue, and he pointed out that this variable applies to a database, and your script could easily set ORA_HOME at any time before loading the database
Thanks,
-Wade