Software programs for individuals. Oh, maybe when you come across something you think is important while browsing the web you could highlight it and these things would be presented to you occasionally sort of like a "drill" to make sure you don't forget it, or prime association formation at a later time.

Congratulations, you've nearly reinvented spaced repetition! There is a great deal of writing on spaced repetition flashcard systems, so I won't inflict upon you my own writings; but the Wikipedia article will link you to the main programs (Anki, Mnemosyne, and SuperMemo) and some writeups of the topic. SR is a great technique; I love it dearly.

Or some short-term memory aid that works better than scratch paper.

Well, you could just improve your working memory. Unusually, working memory is plastic enough to be trainable by WM tasks. The WM exercise I'm most familiar with is Dual n-back. I practice it, but while I have noticed improvements, I'm unsure whether they repay the time I've put into it; SR systems have proven themselves as far as I'm concerned, but the jury is still out on dual n-back.

Or taking a cutting-edge knowledge representation framework like Novamente's PLN and trying to enter stuff into it as an "active" note-taking system.

Now that sounds interesting. But looking at this OpenCog link doesn't give me a good idea as to what PLN might do for note-taking (or really, in general); did you have any use-cases or examples?