Story Told in File Names

This picture was taken from www.phdcomics.com (by Jorge Cham) showing one of the common scenario encountered by PhD students which is having a lot of modified and updated files in their computers. This situation is exactly the same as mine especially for students who involve mainly in programming and simulation. From the above picture, you can see that there is like a story behind how the files were named. You will know the file is not working when you see bad file names like @#!#$%, crap and arrrggghhh hehe. Finally you might want to rename the file as the one which is the finalised so that you can use it as reference when writing the thesis or journal papers (for example like the file name USETHISONE in the above picture). Currently, I just rename the file according to the date the file was created like manuscript_110710, program_040810 etc, so that I will know which one is the latest one. Any suggestion for a better way ?

Currently I have a lot of modified and updated files in my computer and sometimes I do get confused when trying to retrieve the needed information. However, I have just rearranged and cleaned all the unwanted files and now it is much easier to find the files that I need. I think I need to take some time like once a week to manage the files properly. One more thing that is important to think is how to keep the files securely.