Develop Reference

Is there an HTA-like solution for modern web apps?

I have been developing an app using HTML, CSS, and JS, using the App Mode command line argument for Google Chrome. It works nice, but I would like some ability to use the local file system without manual input from the user. That is, if I want a file accessed directly, I want it automatically done, not requiring the user to load the file in.
One option is to disable web security, which I'm not doing because there is a need to use Google Chrome normally. I haven't been able to use a command line argument to create a separate instance of Chrome, either.
I tried working on an HTA, but any attempt to port the code to HTA ends in headaches. Also, it doesn't seem to enjoy the perks that Blink/Webkit grants.
I looked into Electron and other similar platforms, and it requires installing a handful of things, which is a no-go due to the computer setup.
Are there any solutions with a sort of portable app, that can be dropped in a folder with the HTML document (say, labeled index.html or main.html), and upon opening the browser it directly opens that file without having to configure anything? A sort of barebones chromium-based browser that only opens a single file, allowing use of HTML, JS, CSS, along with local file access? Kind of like HTA but modern?

The good news, is that it does exist, but it's not as "out-of-the-box" as HTA.
My team has migrated from HTA to WebView2.
The overall approach is to build a program with the WebView2 browser (you're basically building your own HTA like browser). Your javascript code can communicate back and forth with the program, which in turn has full access to local resources.
WebView2 is the Microsoft Edge Chromium browser, so you're getting the latest web tech and layouts (a big pain for HTA dev.). The program that contains the WebView2 control has full access to local files, scales, printers (without a pop-up dialog).
The approach has all the benefits of HTA (html / javascript programming, local file access, web based deployment, etc.), plus all layout and other benefits of a modern browser.
The program you'll build is very small, especially compared with the HUGE runtime of similar solutions, like Electron.
Rick Strahl has an excellent article on WebView2, and tips for building the program I'm describing. He has great advice on how to build an installer for it, including "Evergreen", which keeps the WebView2 up-to-date with the latest browser tech.
Microsoft's introduction to the technology here.
https://learn.microsoft.com/en-us/microsoft-edge/webview2/

A Productive Javascript/Phonegap Development Environment

I've been building Android apps for a few years now, and I've arrived to this working setup:
Intellij Idea IDE write/debug
Genymotion "Emulator"
Physical Device (only when needed)
Git
Ant (probably should move to Gradle) Release/Debug builds
And now I'm looking to form an equally productive environment for Javascript (Phonegap, etc), for Android/iOS/Win8Phone.
I want to avoid the "nice-text-editor-only" solution (I believe a full IDE is superior in productivity terms).
Any suggestions?

Try Brackets editor http://brackets.io/. It's a nice editor to code the web. Phonegap plugins also available for this editor. Just take a look at this editor. Make sure to download the version of Brackets with Phonegap Plugin compatibility.

For the Cordova/Phonegap app I developed, I used cloud9. In my workflow, I would first get things working in my browser, then occasionally do builds with Adobe's Phonegap Build service to work out the kinks on my mobile devices.
The nice thing about c9 is you'll have a public URL for the website you're developing so you can preview it in your device's browser, which is typically closer to the environment you'll get with Phonegap.
The weinre debugging tool, although slow if you're running it through http://debug.phonegap.com/, can really help track down problems when debugging on mobile devices.

Can I write an app in javascript/HTML/CSS and sell it on the app store, google's play,and microsoft mobile app store?

I am interested in web standards (js/HTML/CSS). I would like to create applications from them, for phones and tablets. And sell these applications on mobile stores and web stores (for appstores and google play).
Is it possible ? What would be the best way to do it ?

Yes, there is a PhoneGap platform that can be used for building mobile apps for iOS, Android, Symbian, Windows Phone.Apps developed with it are accepted in all the stores. It is quite popular, robust and has nice features.

As mentioned in one of the other answers, yes PhoneGap will do the trick if you decide to write your app in HTML/CSS/JavaScript. Now, if you want to have a pleasant user experience on both smartphone and tablet operating systems, I would also recommend looking into Twitter Bootstrap.
This CSS framework has built-in responsive web-design styles that will allow you to scale things down in a user-friendly manner from tablet to smartphone, as well as show/hide different parts of your HTML depending on whether your users are viewing the page on a tablet or smart phone.
Specifically, you can do things like the following:
<div class="visible-tablet">
This will only be visible on tablets.
</div>
<div class="visible-phone">
This will only be visible on smart-phones.
</div>
For a full listing of the responsive design support in Twitter Bootstrap, check out their section on responsive design.
You may also want to check out the Google Chrome Web Developer plugin to assist you in creating a responsive web experience. This plugin lets you (among other things) view how your page will look on multiple device resolutions and is an invaluable tool for debugging resolution-specific issues.

You can look at Zurb Foundation, which is a very active open source project for building responsive web apps for mobile devices. Some overall description of the features here.

You can create Windows 8 Apps using Javascript and HTML 5 (apart from using Native languages). Windows 8 runs on Surface tablets and PC's.
Create your first Windows Store app using JavaScript (Windows)
There is a free ebook as well: free-ebook-programming-windows-8-apps-with-html-css-and-javascript

There are lots of options around - PhoneGap seems to be the most popular and, since it's now part of Adobe, it will probably continue to be popular.
However, there is a more important issue to be considered here: iOS users expect an iOS app experience, Android users an Android one... You get the idea. Make sure it's the best choice for your customers.
See this story about HTML5 at Facebook.
Also, and I know I might open a can of worms here, the performance will always be inferior to that of a native application.

You can also try MoSync:
"Build native mobile apps for all the major platforms using our leading open-source, cross-platform development environment. Now with support for In-App Purchases, NativeUI and Windows Phone 7." ]

There's Titanium from Appcelerator where according to their site you can build native apps using Javascript.

Just a late update: Facebook has open-sourced react-native since use asked your question and unlike PhoneGap (now called cordova) React-Native does not build hybrid app but builds true Native mobile application with the same power you would get when using Java for android or ObjectiveC for IOS. You can find out more here

No point in doing Microsoft/Windows Mobile anymore since it's now dead, but the easiest way to create Android apps based on HTML is to use DroidScript which can be found on Google Play (it did not exists at the time of this question).
You can also build native (non-html) apps with pure JavaScript using the same tool and it's far easier to use for novices than PhoneGap/Cordova.

Developing a cross-platform self-contained HTML application

I am thinking of building an application, kind of like TiddlyWiki in the sense that everything is self-contained in an HTML file, or at least in a bundle where a user won't have to install anything. It works on just about any browser, and on mobile phones (Android and iPhone), and in some browsers (e.g. Firefox), manages to save to the local filesystem without a plugin (albeit, it launches many security warnings, but there are other solutions for that). Other browsers happen to use a Java plugin to bypass this restriction.
Are there any technologies that exist that make this possible? HTML5's web storage sounds like it would be almost perfect, except that the data would be tied to the browser.
Any assistance would be appreciated (even if that just means editting / retagging the question to get more folks looking).

Whats about the fileapi: http://caniuse.com/#search=fileapi

I am just adding a relevant comment with this but not exactly an answer...
When you are saying that you want to develop application which contains everything... Then I would like to add about Titanium, PhoneGap, and others (Corona)...
This softwares provides JavaScript base which will be running on all the mobiles (if mobile applications), desktops (if desktop applications) and so on.... But Titanium (as i am working on it) works on the SDK of all the other languages for development...
Now TiddlyWiki, what i have understood from the link is that it is creating a web application or something like that which will work on all the other mobile devices. But this is NOT Good always, Since some application needs to be a NATIVE environment (which is supported by Titanium). Native applications will be much more faster than any other developed applications..

Desktop application development with Javascript and HTML

I am looking for Titanium Appcelerator alternatives for Desktop application development with HTML and JavaScript. I want to convert a web app to a desktop application. Hence, there will be a lot of server interaction. Appcelerator was a good choice, but it looks like the company is no longer interested in the Desktop SDK. Also, ajax request from Appcelerator does not retain cookies.
I read that Adobe Air can be used for desktop app development, but I don't want to use flash.
How good is XULRunner? Will it allow features like Growl notificaiton and creating tray icons?
Will I be able to develop applications using mostly Javascript and HTML in Qt?

I started looking into Titanium for desktop dev. I liked the concept but not the implementation. I then stumbled upon chromiumembedded and have been mostly very happy with it. It's basically a web browser control based on chromium.
http://code.google.com/p/chromiumembedded/
It's written in C++ so you can do all the low level OS stuff you want(Growl, tray icons, local file access, com ports, etc) in your container app, and then all the application logic and gui in html/javascript. It allows you to intercept any http request to either serve local resources or perform some custom action. For example, a request to http://localapp.com/SetTrayIconState?state=active could be intercepted by the container and then call the C++ function to update the tray icon.
It also allows you to create functions that can be called directly from javascript.
My biggest challenge has been debuging. It's very difficult to debug javascript directly in CEF. There's no support for anything like Firebug that I am aware of.

Appjs (appjs.org) looks very promising.

You could also check Bowline which is another alternative: http://bowlineapp.com/.

Although it's not officially intended for general-purpose use, a number of people have had success using brackets-shell for HTML/JS desktop apps. It embeds Chromium (CEF) and adds APIs for menu bar management and file IO. It also embeds an instance of Node.js so you get access to all its APIs for launching processes, etc. It's MIT-licensed and available for Mac & Win, with a Linux version currently making rapid progress.
As I mentioned, it's not officially a general-purpose app shell, but someone wrote a detailed blog post about how to customize brackets-shell for your own uses.
I notice that the other answer about Titanum says CEF is hard to debug. I'm not sure if that's true in Titanium, but in brackets-shell it's easy to debug JS – you just open http://localhost:9234/ to load a full instance of the Chrome Developer Tools (including breakpoints, profiling, etc.).

TideSDK is a continuation of the old Titanium desktop http://www.tidesdk.org/