In all the Apple "Office" apps - Keynote, Numbers, Pages - there are a number of standard colors that can be picked from the popup. These are different for every theme. This looks as follows. How can these colors be changed?
OS X Mavericks (10.9)
WOW!
This is a fantastic answer. It took me a bit to figure out that this can only be done if you click on the color box that DOES NOT have the colour wheel next to it. You need to use both the plain fill box, and the color wheel fill box. This really could have been done much, much easier by just letting you drag and drop from the colors picker to any color fill box.
For anyone wondering, you can do the same for the gradient fills and the image fills, by choosing one first, then dragging to the fill box as above. Oddly, none of the various shades are pre-calculated so you could have a palette of 29 colors (why not 30??)
Apple developers - this really needs some work.
In the style fill Inspector, click on the multicoloured circle to open the colour palette, select the colour you want to add to the colour fills.
Click on the current fill patch, then drag down on to an existing patch to replace.
The new colour fills will be saved with the presentation and you can create a custom theme to use for other presentations. (File > Save Theme)
How to change default keynote colors
