This is really a broader topic. You first need to decide upon what is the objective. Whether its high availbility or disaster recovery. Also, there might be varying components which need to be backed up. typically ther could be following strategies:
Level I- Cold backup
Level II - Combined Cold and Hot backup
level III - Snapshot backup of ALL primary repositories.
Component to be backed up:
1. Database server
2. Vaults
3. LDAP
4. Remote site cache and Master vaults
5. Cognos if installed
6. Secondary repositories like search indexes
7. TIBCO transactions if ESI is used
You can refer to the Windchill Backup and Recovery planning brief document on PTC.com
Hope that helps
Regards
~Syed