One of the primary stumbling points in my search for a personal note management system that I can carry with me through at least my next year of college has been equations. After a couple of days of looking at various solutions, I settled on using LaTeX. Fortunately, I found a good page covering how to download and install base TeX packages on Mac OS X, as well as offering links to various front ends.
I would have preferred not to go this route - LaTeX is not a terribly easy system, particularly when all I need is the ability to enter different equations and formulas into my notebook. But the only commercial offering I could find cost twice as much as the Note Taking application that I'm getting closer to buying. I've considered writing to Aqua Minds suggesting that they include an equation editor with NoteTaker, but decided against it. Generally, I like applications that specialize in their offerings. It seems to be a very Mac thing to do, especially in Mac OS X. But the tight integration offered by the lamentably axed OpenDoc is still missing.
One of the TeX front ends that I came across give me hope, and that is EquationService. "Services" are an age-old NeXT technology that let applications offer new functionality to the whole system, and are still present in Mac OS X today. Nicely, more and more applications are starting to offer them. EquationService takes the cake though. What it offers is the ability to enter TeX in any application that supports Services (almost all Cocoa applications, and some Carbon ones as well). The LaTeX source can be selected, and via the "Services" menu one can select "TypeSet Equation", and the equation will be replaced by a fully typeset image. Basically, this adds TeX support to any rich text application in Mac OS X. It's not OpenDoc, but it's close. It fits in nicely with NoteTaker, which didn't take too kindly to some other TeX editors which generated PDF's that could be dragged and dropped. Since they would always get dragged with the same file name, NoteTaker seemed to get confused when you had more than one dragged in.
Another feature that Equation Editor has is that it embeds the source used to generate a PDF inside of the PDF, so that it can be extracted ('untypeset') inline to edit the source of the equation. Application support for this seems to be a bit squirrelly. For example, in TextEdit, this feature is supported if a rendered equation is dragged and dropped out of the EquationService's editing window instead of having been generated inline. Other applications may fare differently.