This is probably part of a wider discussion (do you use your company email or personal email address on a public forum, for instance)
At Fedict, we have indeed an organizational account on github (https://github.com/Fedict/), and I'm also using my personal account. Although not carved in stone, the github "rule" that I use is that I use the organizational account for projects that are work-related, however small. So I use my personal account for things like Coursera-assignments and hobby-projects.
Sometimes I voluntarily "promote" a project from personal to organization (never the way around), because some hobby project becomes somehow interesting for my organization.
But it really depends on the project for existing projects:
Fedict also has account(s) on drupal.org for hosting Drupal-related modules and distributions. Now the Drupal.org community encourages individual accounts (instead of organizational accounts), to make it easier to give credit to individuals (and to check code quality I guess).
So I think it boils down to:
- use the organization account if it has the potential to be reused and/or is done during work
- make sure there are at least two people that have full rights to a repository (just in case someone is not available / leaves the organization etc)
- if an inventory is desired, simply create a page / website / document in your organisation listing the links to the different repositories (and make sure the list is maintained / updated)