The VIVO directory. This would include the VIVO code installed, images, uploads, etc...
The VIVO relational database
The VIVO RDF store
Step-by-step guide
Things to think about
If you've made changes to code, make changes to ?freemarker? files, etc... then you might want to consider branching the VIVO and VITRO github repositories. This would act as a "backup" of any changes that you've made and backups would be handled by, say, github