Brad - just a couple ideas I have on File System deployment vs. msdb is:

1) I don't really like having packages floating out there on the server - seems much more secure to have them inside the database

2) If they are in msdb, the packages can be backed up with the scheduled sys backups

3) Don't have to worry about roles/passwords/proxies etc.

Just my thoughts though. Everyone has there own preferences.

Sorry for getting a bit off track Robert....thanks for the informative article!