<p>I'm a long time hobbyist programmer interested in getting into web application development. I have a fair amount of personal experience with various non-web languages, but have never really branched over to web applications.</p>

<p>I don't usually have any issues learning new languages or technologies, so I'm not worried about which is the "best" language or web stack to work with. Instead, I'd like to know of any recommended resources (books, articles, web sites, maybe even college courses) that discuss web application design: managing and optimizing server interaction, security concerns, scalability, and other topics that fall under design rather than implementation.</p>

<p>What would you recommend for a Standalone Application Developer wanting to branch out into Web Development?</p>

A lot of languages have web counterparts. JSP for Java, Rails for Ruby, Django for Python, etc. That might be a lead.
If you want to go for the platform with arguably the biggest user base (and with that, the biggest pile of tutorials and examples), go for PHP.
I strongly advise on looking into various frameworks though. For every web-oriented language there's bound to be a lot of resources that take away the trouble of writing all the low-level plumbing code, so you can focus on the stuff that matters. Personally I almost exclusively use .NET, but I've heard about a bunch of nice PHP frameworks, like the Zend platform and CakePHP (for MVC development).
If you intend to also use javascript in your applications to give that nice web 2.0 feel to your applications, please, use a library that hides the messy browser details. You'll go nuts if you try to do all the cross-browser scripts yourself. Some good ones are Prototype and jQuery.