The following site provides a description of the pros and cons of each:
http://pragmaticworks.com/community/blogs/nayanpatel/archive/2008/11/13/what-are-the-advantages-disadvantages-of-storing-ssis-packages-to-msdb-vs-file-system.aspx
This is summarised in the following table:
Functionality Best in File System Best In MSDB
Security Yes
Backup and Recovery Yes
Deployment Yes
Troubleshooting Yes
Execution Speed Yes Yes
Availability Yes
Where i work we have a number of different shipping environments, and shipping tool. We also have the need to pass in connection strings (for each shipping stage), so have to worry about other means by which we encrypt the data. Placing everything in the file system is so much easier for us.