How to architect a website's presentation layer?

Question

I have been going back and forth in different approaches for designing the presentation layer for websites.

Many people swear by one of the different CMS packages which is too constraining and inflexible. Many people suggest writing the HTML by hand which seems not to scale in the case of many pages.

I have a new web application I am designing and I really want to have a "correct" and "elegant" and practical approach in how I architect it.

Has anyone done this in a way in which they are happy with and can plug in various modules and libraries with no problems?

Any tips or pitfalls I should watch for?