The basic command to create a self-signed certificate is:

adt -certificate -cn name [-ou org_unit][-o org_name][-c country] key_type pfx_file password

so a working command to create a certificate could be:

adt -certificate -cn ID8 1024-RSA devCert.p12 certpass

For more information on code signing certificates check out:
Creating a self-signed certificate with ADT
Digitally signing an AIR file

Packaging An Adobe AIR Application:
The Adobe Documentation has all the information you need to package an AIR html application here:

Packaging an AIR installation file using the AIR Developer Tool (ADT)

The command I used for this project was:

adt -package -storetype pkcs12 -keystore path_to_certificate testapp.air path_to_xml_descriptor_file .

The main bits you’ll need to get a HTML AIR application going are:

An application descriptor XML file:
There is a template of this file in the templates directory or a sample file in the samples directory.
Copy the descriptor-template.xml or descriptor-sample.xml file from the templates or samples directory to the application directory you created earlier (in this example the Applicationstestapp directory. This descriptor file can be called anything, I renamed mine to application.xml

The files to make your app do something:
Things like html files, images, javascript, style sheets etc. All these files go into the application directory you created earlier and everything needs to be referenced relatively.

The structure I ended up with in my testapp directory was:

    testapp
        icon
        images
        scripts
        styles
        application.xml
        index.html
        login.html

Frameworks
You may also want to use some of the files Adobe supplies in the frameworks and samples directories. See the Readme.txt file for descriptions of what’s in these directories.

I used from frameworks:
AIRAliases.js – Provides “alias” definitions that allow you to access the AIR runtime classes from Javascript.
AIRIntrospector.js – Assists in AIR application development, allowing you to inspect JavaScript properties, view the HTML DOM, and view source files at run time.

I used from samples:
badge – A directory containing sample files for the AIR seamless install feature, which lets you distribute an AIR application directly from a web page.

Command line tools:
You will use these to create self-signed certificates, to test and compile your apps.
These are in the bin directory of the AIR installation.
adl (adl.exe on Windows) – The AIR Debug Launcher (ADL) allows you to test an AIR application without having to package and install it.
adt (adt.bat on Windows) – The AIR Developer Tool (ADT) packages your application as an .air file for distribution. This is also used for creating self-signed certificates.

What I wanted:
- Simple Application to enable a user to log into a website and deliver some content.

What it needed to do:
- Install using a web based installer.
- Be cross platform (Linux, windows, Mac).
- Be set to run at startup as default.
- Run as a taskbar/Dock application.
- Notify the user when there was an update for the application.

Installation and Familiarisation.
Get the Adobe Air SDK – http://www.adobe.com/products/air/tools/sdk/
Once extracted you will have a directory structure like:

AdobeSDK
    bin
    frameworks
    lib
    runtimes
    samples
    templates
    AIR SDK Readme.txt
    SDK licence.pdf

I added an additional directory for application files to the above structure.
The Applications directory is where you will put all the application specific resources for your applications.
Say we wanted to create a new application called testapp, we would start by creating a directory under the applications directory and putting all the application specific files in there.

    Applications
        testapp

The AIR SDK Readme.txt is a good place to start to get a feel for what is required in creating an AIR application.

You should also get familiar with the following doco:

Developing Adobe AIR Applications with HTML and Ajax
http://www.adobe.com/go/learn_air_html

Adobe AIR Quick Starts for HTML
http://www.adobe.com/go/learn_air_html_qs

Adobe AIR Language Reference for HTML Developers
http://www.adobe.com/go/learn_air_html_jslr