I am a huge fan of TimeMachine (the Mac OS X backup solution) and I like the approach of archiving whole files. The only drawback occurs if you have huge files (e.g., hard disk images for virtual machines) that are often modified.
Here a way to reduce the backup size of your VirtualBox hard disk images: simply create a snapshot of your machine. VirtualBox will then leave your hard disk image untouched and create a separate file with just the changes from the time of the snapshot.
When the snapshot becomes too large you can merge it and create a new one (by choosing delete snapshot the difference file will be merged with the hard disk image).