I’ve recently come to the conclusion that I’m unlikely to use Themes in SharePoint again in a hurry. Why?

• Themes allow you to provide a bunch of CSS styles. So does the AlternateCssURL.
• Themes have to be applied site-by-site (unless you do some programming, or extend STSADM). Alternate CSS or Master Pages can be changed for a site and subsites, for a Publishing site anyway (although with some limitations).
• Alternate CSS can be provisioned from a single URL – so benefiting from browser caching just like images.
• The Alternate CSS can style the DatePicker. Themes can’t.
• The Alternate CSS can style Application Pages, just like Themes (but unlike Master Pages).
• No problems with ‘Style Merging’ when the Theme is provisioned.
• Style can be updated in one location.
• Themes can be changed through the UI for any site. Only Publishing sites have a user interface for changing the Alternate CSS.

Yes, many of the same distinctions between Master Pages and Themes still exist, and the same sort of analysis and choice of approach should be done. However, it means that we can kind of ignore Master Pages, and just focus on Alternate CSS vs Themes – and it seems to me that apart from the last point above, the Alternate CSS approach seems to equal or better than Themes.

Regarding the last point, well, to apply my theme I’d set the Alternate CSS in a Feature Receiver. This is okay, though, as I’d probably be writing one anyway to apply the correct master page to different types of site.

So, the answer I’ve come to now – I’d use the _layouts directory – create a sub-directory for your brand, and put your CSS and images in there.