publications - Archiving papers, simulation and experimental data, etc?

Archiving of papers and projects is very important for most of the people, and everyone has a method of it.

I, personally, try to have different folders for different papers. In the folder of each paper, in addition to my manuscript, I keep my simulation files, experimental data, program codes, etc, in different subfolders. Also, I try to keep track of my revisions on the paper, reviewer comments, my response to reviewers in different subfolders. My method has the advantage of all the related material for a paper are together, and I can quickly track the whole process from initial submission to the final proofreading. However, this usually leads to duplicated files.

I work with both my office desktop and my personal Laptop. I transfer my files between these systems by a flash memory. I agree maybe cloud technology is a better choice in this age, but I postponed it because of my poor internet connection at home.

I am curious to know how others approach to archive their works. I also hope to find some methods more efficient than mine, or get some tips to improve my method.

Edit at 2 Apr 13: Thanks to these great answers, it is almost a month that I use Git for my version control. Also, I manage my repositories in the Bitbucket, which gives me unlimited storage for unlimited number of projects.

Answer

I have a similar approach with folders, with two additions:

1. 
   

   Everything goes into a revision control system. In my case, I've got some things in Subversion repositories, and others in Mecurial repositories (I've also dabbled with Git, but haven't made the final transition). The benefits of revision control are that you can always go back to a previous version, you won't have old versions littering your folders, and sharing with collaborators is relatively easy. This should take care of your duplicated-file problem.

   
   


2. 
   

   I also use Dropbox extensively, in order to have my files available on any computer at any time. Dropbox provides a modicum of version control (30 days worth), but it should not replace a proper revision control system. It does provide a cloud-based backup of your work.

   
   

   Finally, regardless of how you're keeping your work arranged, make sure you keep an off-site backup (e.g., via Dropbox or personally-controlled media).