I like my technology, so I am opting to store my notes and work in the cloud. Both Evernote and GOogle Drive make my work available to me from anywhere at any time, even on my iPhone and iPad.
Evernote (that’s a referral link, if you sign up, I get points)
This is my choice. I can type notes, easily clip websites, import PDF files. I can handwrite notes in Penultimate on my iPad, or snap a picture of a handwritten document, and Evernote can recognize my handwriting (ish). It is searchable, and it mimics the real world enough that it makes sense to me. I can access my notes from anywhere at any time.
I use Google Docs and Sheets quite extensively at work, and can also see that if someone took the time to set up notebooks, it could be very easily be used as a great notetaking solution.
I’m pretty far removed from the Microsoft ecosystem, that I don’t know much about OneNote, but I suspect it fills a similar role as Evernote or Google Drive.
There are different ways to approach a portfolio. Perhaps the notetaking and storage you are doing in Evernote or Google Drive is sufficient, but if you want something more formal to show off, you can consider a few options.
Accredible or Degreed. These are just two of the sources I have found that let you create portfolios of the classes you have taken in a formal way. They display certificates of achievement. Both are also really good sources for classes that are available.