Doing a corporate website redesign. Usually unique templates would be identified and those are the pages that would be wireframed instead of having to do every single page. What happens if the website isn't so much templated and is more modular. How does one decide what needs to be wireframed?
It's all about the site objectives regardless of the site being modular or templated. I guess there aresome standard templates still around such as Organization Page, Cooperation Sites, Controlled Documents Library, Knowledge Sharing and a couple of other standard (templated) landing pages. These pages can probably not be completely modular letting user chose wheather or not to show controlled documents, or delete a message board. Parts of these pages can certainly be customized and modular - but not all of the page.
Wireframing modularity would be no different than a templated site. You'd probably need a layout for the page - and each possible module, unless the modules themselves are templated. If it's possible to change size of the modules you're also going to need different layouts for each possible size.
If that's not possible due to the time you need to invest (and you're customer have constrains in their budget), make samples of different scenarios showing the most of your ideas. That way your customer gets the wireframe design idea rather then the exact design in wireframes.