We don't really have a 'Best Practice' guide for key management. NIST has published some recommendations via document SP 800-57:
http://nvlpubs.nist.gov/nistpubs/SpecialPublications/NIST.SP.800-57pt1r4.pdf
My recommendation would be to use Server Key Mode (SKM) keys if possible, to reduce reliance on end users and provide more management ability. These should be tied to Active Directory with AD Synchronization. The keys are distributed to the users as needed, and the users can be blocked from modifying the keys.
If using FileShare, I would also recommend using Group Keys, so you can add and remove users without any manual input on the server or on the shares themselves.
In the end, it really comes down to business needs, potential government regulation (particularly in European areas, where they may govern the signing key requirements), and ease of management. In most cases, SKM keys are preferable, but they may not be the best choice depending on what you are trying to accomplish.