The answer to the question above is very much a question of security. I am facing the same question at the moment, I believe it would be best to move all CFC’s into a globally accessible shared mapping. From here the CFC’s can then be divided by project or use, similar to Java notation for a package. E.g.
Obviously moving these objects out of the web root would have an impact on any method within the CFC, that is being accessed as a web service. I found a handy comparison matrix on Adobe Live Docs for ColdFusion 8, that will help you when making this type of decision.