We use MOSS 2007 (SharePoint) for our intranet. Recently we were tasked with supporting the branding for multiple companies on our farm. We quickly realized that the application pages (produced by a modified application.master) can't serve up multiple branded templates (other than themes).
I think the right fix is to keep the default Microsoft branding on application pages (we were already working on this in dev - no modifications to files hosted on the server).
As a quick fix however, I was thinking that I might be able to use jQuery to replace one logo, a handful of nav images, and a few colors on the application pages. Basically going from Brand A to Brand B before the page is fully rendered.
My question is... how bad is this idea? What are the pitfalls associated with doing this? Given that it is only an interim solution, should I try it?