<p>I have custom coded several enterprise applications for mid to large organizations to use internally (some with a minimal external footprint).  I now have plans for a web project that may (hopefully) see a large userbase with more daily traffic than my previous projects have ever attained.  Obviously I want my design to be scalable and maintainable.  The problem is that from a physical layout perspective (servers/VMs) I do not know what to expect.</p>

<p>The question:  What are some good resources for this?  Books?  Websites?  I have found plenty on scalable application design, but nothing on scalable physical design.</p>

It's hard to give exact answer without knowing something about what technologies you plan to use. The approach to the application can't be completely unaware of planned physical infrastructure if scaling is a major driver.
Caching would have to be a big concern.  Also ways to expand the hardware where your data lives.
A very interesting and instructive read is the real world bio of live journal,
a history of scaling
, and how they grew their physical presence with a massive growth in their website.  One major offshoot of their work was a new caching technology, memcached, which is now used by FaceBook among others.  It is surprisingly honest.