I have some guidance on how to organize data (written back in 1999), but these guidelines are far superior. To be honest, you should use a database for anything more than half complicated, but for those simple data sets where you can use a text file or a spreadsheet, Dr. Broman’s comments are very helpful.
Karl Broman. Organizing data in spreadsheets. Available in html format.
You can find an earlier version of this page on my blog.