I am running windows and use acronis. I make daily differential backup and weekly full backups of my projects to a separate disk. I can't afford offisite or network solutions like carbonite. But I do have separate disks to store all my project backups and system/software images.

Whenever, I make significant changes to software on my system I use acronis to make an image of my system disk. I keep my data/projects on a separate share then my OS. This way system images are just the os and software installed on the system.

Unfortunately storage is finite so I just keep my current system image and the last one or two images and I have been bitten a couple times when something sneaks in undetected and I have imaged the disk a couple times and the last clean image has been deleted. But in almost all cases I just had to identify and remove or fix the problem in the current setup and then make a new image.