Thanks for the excellent question.If you're running the free version of s2Member, the easiest way is to upgrade them manually through your WP Dashboard. You can find them in your list of Users in the Dashboard, and just give them one of the s2Member Roles [1-4] and click update. This way they're upgraded without paying.
If you're running s2Member Pro and you have a LOT of these to deal with, you could use s2Member Pro's advanced Import/Export tools, which also supports mass updates to existing Members. This would allow you to upgrade many Members all at once, by simply importing data with s2Member that reflects a new ( i.e. higher ) Membership Level. For further details on this, please check your Dashboard with s2Member Pro installed, under:
s2Member -> Import/Export.
You may also find this interesting. This is an excerpt from the release of s2Member v3.5.3. There is some new functionality available for s2Member Pro's Free Registration Forms that was not possible before. * **(s2Member Pro). Feature improvement.** s2Member Pro Forms for Free Registration access are now more versatile. It is now possible to configure your Pro Form Shortcode so that Free Registrants come into your site with something other than the default Level #0 Access Level. For example, if you need to, you can change the Form Attribute `level="0"`, to `level="1"`, attach Custom Capabilities with the `ccaps=""` Attribute, and even limit this access to a certain timeframe with `tp="30" tt="D"` ( i.e. 30 Days ). So this Form is very flexible now. It can be used to allow free access to just about any aspect of your service. For more information on this topic, please check your Dashboard under: `s2Member -> PayPal® Pro Forms -> Free Registration Forms`. Also works with Pro Forms for Authorize.Net®.