GCF is a VALVe prioprietary file format and is not documented. There is no way (at the moment) to create GCF files, and even if one is created, Steam might not even recognize or use it. GCFScape has some GCF reading and defragmenting habilities, but that's about it.
The SourceMods folder is there to accomodate mod creators since they can't create GCF files.