The Internet is a dirty place and only a fool attempts to give it a clean.
As you progress on your online adventure you learn as you go and that leads to many experiments that are either abandoned with good cause or left to wither and die long before they have had a chance to bear fruit.
This leads to your little world becoming very dirty.
The temptation is to clean or re-organize your Internet habitat which may seem like a good idea.
However, your idea has a large downside.
Previously to this point, I assume you had a honeymoon period with everything you created online, a period where you loved telling people all about it.
And, of course, the more that heard about it, the more Internet lifeblood you created.
The lifeblood of the Internet is links.
Every piece of content on the Internet is linked to by another point, it has to be otherwise the Internet would cease to operate.
However with your urge to be more organized or wipe the slate clean you are stopping the blood flow of the Internet in its tracks, both the search engines and people hate to see what you have created.
You have created broken links.
So what are you supposed to do?
The best options are to leave those domains in place until they die a natural death on their renewal point meanwhile redirecting any visitors that stumble upon them to a place more current and relevant to their area of interest.
For sub-directories on your sites that you still love, why not replace the abandoned content with optin pages or redirects to current content related to the original forlorn content.
By adopting this strategy, you continue to make the most of your previous traffic generation activity whilst keeping in the good books of your audience and the all powerful search engines.