That's not to say that a tremendous amount of UX + graphic design, development, and testing are involved - they are, which I celebrate.
But I'd like to suggest that the end product of "HTML 5" app development (assuming any HTML 5 is involved at all) more closely resembles mobile development than desktop application development. I'm uncomfortable with the notion that browser + Javascript-based applications should be considered on-par, feature-for-feature, experience-for-experience replacements for desktop applications written in native code for specific operating systems.
Please don't get me wrong - I'm not attempting to channel a neo-luddism, or pining for the days of Swing and QT. There are tremendous advancements being made in the browser. But browser-based applications are constrained to running inside a browser. Development for browsers is painful and wildly inconsistent, unless papered over by frameworks we all love like jQuery and Prototype. We're heading closer to native implementations of animation and media-related functions, but are still years from any sort of standardization. Even companies heralding the era of HTML5 + JS + standards...well, fragrantly undermine their points by releasing single-browser demos and calling it "universal" (see Apple and the recent HTML5 demo flap).
I look forward to the day when web and browser-based development are a breeze. But until then, I'd feel much more comfortable referring to such endeavors as "web apps" and "web sites" than "applications" in the desktop sense.