Safety Net (available in Deja Vu 3.1 or higher) adds support for versioned backups. See the Safety Net tab in the Options sheet.
When Safety Net is enabled, changed and/or deleted files will be archived in the Safety Net folder, which is located in your Documents folder by default. Safety Net archiving will happen before the actual backup begins (i.e., before any files are copied). You can keep as many of these archives as you like, which will allow you to go back and retrieve a document as it existed, say, three days or three weeks ago.
UPDATE: Deja Vu 3.5.2 (Leopard), Deja Vu 3.7.3 (Snow Leopard)
Beginning with Deja Vu 3.5.2 for Leopard and Deja Vu 3.7.3 for Snow Leopard, Safety Net will now archive files even when an entire disk (including the startup disk) is selected as the backup source.
When backing up a system disk, Safety Net will only archive files within the Users folder (/Users). Otherwise, it will archive all files as necessary.
EXCLUDING CERTAIN FILES FROM SAFETY NET ARCHIVING
Safety Net is mainly intended to save multiple versions of user-created documents. Therefore, it would be useful to be able to exclude certain items so that your Safety Net Archives folder contains files which are relevant to you. Maybe you don't need or want to save multiple versions of your Apple Mail preferences, for example.
Although there is no user interface for this at the moment, you can still prevent certain files from being archived by Safety Net. These files will still be backed up; they just won't be archived. (To completely exclude files from your backup, see: Excluding certain items from a backup)
To prevent certain items from being archived, use your favorite text editor (e.g., TextEdit, BBEdit) to create a plain text file named "safetynet_excludes.txt", and add the paths to the files and/or folders that you wish to be excluded from archiving, one per line. Save this file in the "/Library/Application Support/Deja Vu" folder.
For example, my "safetynet_excludes.txt" file looks like this:
jeff/Documents/Microsoft User Data
Notice that partial paths may be used. To exclude every user's Library folder, for example, you could add this line:
Finally, remember that files are archived from the backup destination--and not from the backup source--before being replaced by a newer version or deleted if Mirror folder contents is enabled. Therefore, any paths (or partial paths) that you add to "safetynet_excludes.txt" should relate to the backup destination.