The 3 storage options are: Database, Disk and GAC. The main differences between these are:
Database: The assembly dll is stored in the database, rather than the file system. The major advantages are that the assembly need only be deployed once multiple CRM servers are available, and that no additional action is required to restore / redeploy the assembly either during disaster recovery, or if redeploying to an alternate server. This is the preferred option in a production environment
Disk: The assembly dll is placed in the \server\bin\assembly directory on each server. Have to ensure the dll is placed in the correct place on all CRM servers, so the deployment overhead is a little greater. Better to use this option in development environments as the developer can redeploy newer versions solely by file transfer, rather than reregistering. Also, if debugging, the assembly .pdb file needs to be placed in the same location; with this option it’s easy to ensure the dll and pdb are from the same build
GAC: The assembly is placed in the Global Assembly Cache on each CRM server, and again will have to do this. The GAC does allow multiple versions of an assembly, but CRM doesn’t, so don’t really gain anything by using the GAC.
According to my experience deploying the plugin assemblies to the Database is the best option as we can backup and restore the databases and minimizing assemblies deployments and other setting changes.