Almost any introductory PHP book should cover that material in the first few chapters.
Edit for more info:
Oreilly has 'Webmaster in a Nutshell' and there's a 'Webmastering for Dummies' book. These would give you general web knowledge. But the latest edition of the Oreilly book was published in 2002. So it's not going to cover javascript libraries or the latest web application frameworks.
I've just browsed through amazon.com a bit more since no one else has recommended anything for you. Take a look at Oreilly's 'Learning PHP, MySQL, and JavaScript: A Step-By-Step Guide to Creating Dynamic Websites.' That looks like it should cover a pretty full range of technologies and the reasons for each. You can even read the first two chapters online on amazon's site. Though I haven't read it, it looks like the only drawback is that it covers the Yahoo javascript library and not the more popular JQuery library.
Again, I don't think you're going to find anything that is not language specific. The non-specific basic information about building web applications is found in the first chapters of intro books. Non-specific advanced material would be found in books like Martin Fowler's "Patterns of Enterprise Application Architecture."