However, I don't know how to select a font color to match Keynote's master. Perhaps there's a better/free way to create nice equations to use in Keynote and Pages?

There is no equation editor available in Keynote or Pages, but it is possible to creat nice equations in the Grapher application (in /Applications » Utilities) included in OS X, and then copy/paste the equation(s) into Pages or Keynote.
However, I don't know how to select a font color to match Keynote's master. Perhaps there's a better/free way to create nice equations to use in Keynote and Pages?
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Hint Options
Use Grapher to embed equations in Pages and Keynote
You can change the font used. Go to Preferences and click on the the Equations button on top. Click in the "Default Font & Size" window and the standard OS X Font chooser window will pop up. You can select any font and size on your system.
Use Grapher to embed equations in Pages and Keynote
Yes there is. Get Latexit.
http://www.macupdate.com/info.php/id/17889 Actually, it presumes you have a tex installation, but you can just install MacTeX which is really easy to install, includes a full tex distribution and latexit: http://www.tug.org/mactex/ It allows you to type the latex equation, and it will generate a little pdf with just that equation. You can then drag it into keynote, powerpoint, etc.. For those unfamilar with Latex, it allows to type equation with syntax such as: w^{n_{\log_2 m}} which would be w all to the exponent of n with a subscript on the exponent of log base 2 of m. That kind of thing. It's got different fonts/sizes, any greek symbols, about a gazillion operators, etc..
Use Grapher to embed equations in Pages and Keynote
Texfog (http://homepage.mac.com/marco_coisson/TeXFoG/index.html) is a GUI for the formula editor  brilliant stuff
Use Grapher to embed equations in Pages and Keynote
If you know how to use LaTeX, I use LaTeXiT, which produces beautiful PDF format (or other image format) equations, and you can control size and color from within the program, and use LaTeX to vary the font. If you don't, it really isn't that hard to learn; try this introduction (PDF file). To install the LaTeX backend and various frontends (TeXShop and LaTeXiT) with minimal hassle, the MacTeX package is the way to go.
Use Grapher to embed equations in Pages and Keynote
I second this! Plus: if you export PDFs from LaTexit, they retain the text used to create the equation for easy editing later! YAY!
Use Grapher to embed equations in Pages and Keynote
I use EquationService. It hasn't been updated for a few years, but it works just fine. You need to know latex too, but it's got a nice output window, so you can just use trial and error till you get your equation right. Then just drag and drop into Keynote/Pages.
Equation Editor or LatexIt
Three (old) hints on this site:
http://www.macosxhints.com/article.php?story=20030417065555118 http://www.macosxhints.com/article.php?story=20030915192727659 http://www.macosxhints.com/article.php?story=20050209053950215 As others have said, there is now a new program called LatexIt which looks very nice. (I've just started using it recently, and so far, so good.) When I'm writing quizzes and exams for the math classes I teach, I like to make graphs in Grapher. I use Equation Editor or LatexIt to generate equations. I use draganddrop to copy the equations into the Grapher window. Then I export the Grapher graph as a PDF, and include it in Tex using an \includegraphics command. Grapher allows you to change the color and style of curves and points in the figures. I don't do this myself, but it is possible to make the equations different colors as well, using Latex's color package. (Google for "latex usepackage color".) (I don't use color much as quizzes and exams are printed blackandwhite.) It is possible to change fonts in Latex. Google for "latex usepackage fonts". The support is not as simple as one might wish for. In Equation Editor or LatexIt you will have to edit the preamble. Commands like "\usepackage{times}" or "\usepackage{palatino}" (in the preamble) will change the font for text, not for equations. Here is a web page with very good information about math fonts: http://ctan.tug.org/texarchive/info/Free_Math_Font_Survey/survey.html (I didn't know about this till I was writing the last sentence! :) ) Zach
Use Grapher to embed equations in Pages and Keynote
The copied data is just PDF, so you can paste it anywhere that will accept a PDF graphic, including Preview's "New From Clipboard" command.
Use Appleworks
Many of us still have old copies of Appleworks. Under the Edit menu is an option to insert an equation. It brings up something called Equation Editor. Not the greatest but if you have it it's free. This gives you some control of the appearance before you copy the equation to Keynote or Pages. 
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