First of all, I'm a designer not a developer so this may just be a waste of time if the conversion isn't simple.
I am wanting to package the uGet Portable app into a PortableApps.com compatible format.
uGet Portable is actually a .ZIP that contains all of the dependencies and such but it is not in any particular portable format.
uGet is written in C and utilizes GTK+ runtime. Of course, Windows doesn't come with GTK+ so the portable app has it included in the zip.
To launch the portable app you extract the zip, open the "bin" folder and run the file "uget.exe".
Here is the download for the file: http://sourceforge.net/projects/urlget/files/uget%20%28stable%29/1.10.3/...
You can learn more about the app by going to http://uget.visuex.com/
If you need any more information just let me know and I will do my best. I really want to make this PA compatible but I have absolutely no idea how. (I saw the docs but again not a dev)
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One of the best ways to see how to package apps is to download a few of the existing ones and take a look at the structure and the .ini files sitting in the AppData folder. They can often show you how to do a lot of things like run with parameters or set a working folder.
Another way is to take a look at An Unfinished Beginner's Development and Packaging Guide (for overall pointers), PortableApps.com Format (for structural pointers), and PortableApps.com Launcher documentation (for a more in-depth look at everything).
From what you mentioned in your post, you may have already taken a look at the last link. If you run into anything weird, there's plenty of people who can help. Lastly, try to make a version, test it yourself, then post it in the Beta Forums. There, you'll get a lot of useful feedback that will help you learn even more. Cheers!