Like the other guys have said there's nothing that's going to automate this and in most cases the onus is on you. I think the best approach to take will be to list down all the progams that you use and then locate all files on your computer. I'm sure you would know where you keep them and the way to go is to first backup everything that you know and where you saved them. In most cases that'd be fine but you may want to make backups of other things like email, etc, for which it's best if you take this as a step two and then post to the community for help if you get stuck.
The right idea is to mark the apps that you use most and then try to find a way to back them up. Hope this helps!
This question appears to be off-topic because it is asking how to solve a human problem (organization) with a technological solution. No software can decide for you what files are important to you personally. – nhinkle – 2014-10-10T20:15:09.597
What operating system do you use? Windows? – Jonik – 2009-09-19T17:48:21.700
Yes! OS is Windows! – Kevin Boyd – 2009-09-19T17:54:10.923
2No tool will tell you which directories are not required or unused by some installed product. – harrymc – 2009-09-19T18:09:59.380