Formats more likely to be accessible in the future are:
Consider migrating your data into a format with the above characteristics, in addition to keeping a copy in the original software format.
Examples of preferred format choices:
Library of Congress' recommended file formats.
Tips:
Do not go more than 2 folders deep
Each folder should have a README with contextual information
Choose an organization strategy that works for you (thematic grouping/by file type/by analysis)
Simmon's College guide.
NYU's guide.
MIT's guide.
Example:
Directory structure naming
When organizing files, directory top-level folder should include the project title, unique identifier, and date (year). The substructure should have a clear, documented naming convention; for example, each run of an experiment, each version of a dataset, and/or each person in the group.
File naming
Use free tools to help you:
http://www.bulkrenameutility.co.uk
http://www.powersurgepub.com/products/psrenamer.html
File naming conventions for specific disciplines