A very interesting topic in that is coming up more and more today.  A customer wants to customize SharePoint, not just the user viewed screens, but also the administrative (Application Pages) functions.  In many cases, creating customer list templates and web parts to view those lists can fullfill the need to customized the consumable portions of a site, and a bit more effort can be put in to customizing the data entry interfaces that the site's content editors will interface with frequently.

The challenge is that last bit.  In "Teams" or ad-hoc collaboration site generation, it is just not practical to "Wrap" the application pages in that fashion.  We ran in to this very issue, and ended up scrapping (or at least temporarily tabling) a good portion of work for this very reason.  If you haven't read Cameron Moll's Blog Authentic Boredom (He is our lead designer for this effort), he posted a great article there on this problem.

The bit that really chaps my hide, is that we initially heard that what we were trying to do was fairly unique, and others were not trying to do this.  Since then, this has appearently become a much bigger request and frustration to multiple people.

If you've ever heard the MS party-line on modifying system/app files (ie, layouts folder items), you'll get a real kick out of this.  Eric Shupps posted a great article about the new KB944105 (Customizing app pages in the layouts folder).  Yes, you read that right.  Apparently it is now accepatable to do what we are not supposed to do.  Never mind the fact that there are about 400 aspx files in that folder to skin/brand.  It will be interesting to see where this conundrum leads us.