WPF themeing best practices

As Xavier said, this might be a better question for Code Review. But I will convey some key thoughts on your question, even though a lot of it will come to personal (or team) style and requirements.

After creating several dozen themes, I would recommend against custom controls whenever possible. Over time, the maintainability goes down quite a bit.

If you require minor modifications to a style, it is better to use DataTemplates and Data Triggers if the situation allows. This way you are changing the style in a clean way.

Additionally, you can leverage the BasedOn property. Create your "base" style and have multiple styles that have the attribute BasedOn="{myBaseStyle}. This will allow you lots of options without cluttering your code.

As a rule of thumb, I always recommend having more brushes/colors/resources as opposed to more styles or templates. We usually have our hierarchy set for colors->brushes->styles->templates. This helps reuse the colors while still maintaining separation via brushes.

Using DynamicResource as opposed to StaticResource is also useful in some situations where you load resources dynamically.

Hope this helps. Would love to write more, but some of the parameters for writing a solid theme is very context specific. If you have further examples, I'd be glad to add more information.