I'm looking for a wiki engine that lets me highlight sections as I would with a highlighting marker, preferably in at least two colors. I want the engine to be a small installation that is as easy to run as Microsoft Word, such as by double-clicking the document file.
Ok. So you want a personal Wiki. Why didn't you include the ones you've looked at and rejected? Why not tell us whether you want one online, or installed locally? MacOS based? Windows based? Linux? Anything at all to help narrow this down? No?
I mean, you've already cranked up your search engine, and searched for personal wikis... right?
Here's a Lifehack guide to personal wikis.
Now, for example, you could follow this HowToGeek Guide to set up your own TiddlyWiki, and then add the QuickEdit plugin. Once that's all set up, you just click the color button when you write something, and you are typing with a different color font on a different color background... just like highlighting would LOOK, but not like using a highlight marker.
You could follow this Lifehacker article on setting up MediaWiki on a USB flash drive, so it would be portable. But, same essential deal. You'd need to add a more complex editor to it, that would allow you better control at the text box when you are adding information. You couldn't just look at a page of text that had already been entered, and swipe the mouse to highlight it.
But even Microsoft Word doesn't allow for highlighting the same way you would with a marker. I mean, the program itself is relatively complex, you need to type something first, then select it, then use the highlight function. With a Wiki, if it's already typed and on the page/screen, you'd need to edit it in order to change it's appearance. You couldn't just be looking at something you already typed or added, and highlight it.
Of course, if you had a Mac, you could just install VooDoo pad. Less configuration, Mac only, and not free. But hey... that's the trade off for not having to configure it.