StartPortableApps.exe is not quite fully portable, it relies on presence and relative position of "PortableApps" directory.

John,
I am sorry to hear that, the ability to tweak the apps, settings and changing locations while remaining portable has always been what attracted me to these apps.
This all started with a quibble regarding the static requirement for the "..\PortableApps\PortableApps.com\PortableAppsPlatform.exe" Structure and the launcher/linker for the PA launcher menu and a percieved portability issue with a "constant" versus a "variable" location for the portable apps.
It has grown into a somewhat deeper discussion, but I am glad I posted as I learned a lot.
I will concede that changing the portable application bin directory is not a requirement, and by my own logic it really doesn't matter much as it is easy to restore or reinstall, so I can live with that.
It is part of the tool and any programs, libraries or bin files under the "..\SomeApplicatioPortable\" directory need not be moved or movable. (this would include the SomeApplicationlauncher.exe as well as the entire application in the "App" dir.)

Data files (documents) are a different case.
I guess the main problem I have is losing the ability to specify where data and/or profiles are stored.
This is, in many cases, removing or locking out existing core application functionality.

I do wonder why the data is so distributed in PA.c when for years modern OSes and many users have been migrating to a central data storage location, usually in a "User Data" directory.
You even have a central data storage location for application data files, \PortableApps\Documents.
It is just missing all the data directories from all the individual apps but most importantly the complex data rich profiles, like TB, FF or Pidgin which actually contain mostly documents in the form of emails, settings or conversations.

I realize that with some effort the backups and synchronizations can be accomplished in any combination of data storage locations, it just complicates the backup.
It takes about the same amount of effort to move the default save path to a central location as is does to open the backup routine and add another location.
The problem comes in when the backup becomes so complex that updating it or switching to another backup up program becomes a chore and the configuration file to back it up, itself, becomes another piece of data to backup.
When any function, like a backup, becomes too complex, things will likely get missed or remain uncompleted resulting in potential loss.

Many of the apps you mention have less customizations and are easy to tweak and therefore the customization files have less value, some other apps even store no true "data" like the magnifying glass, some only store a few simple parameters.
Audacity, and NSIS will have the ability to save data (documents) to a data location of your choosing, either my Data dir or the standard /PortableApps/Documents so those should not be an issue as long as the default save locations are remembered.
An app like Thunderbird or Pidgin is different in that they have a complex profile storing much irreplaceable data.
This makes the Profile important data as it contains not only sometimes complex difficult to reproduce (remember) settings, but also data you can't get back.

I use Thunderbird regularly and the profile has always been "movable", even before when it was Mozilla, and before that when it was Netscape.
I don't use Pidgin but the default standard data storage location is not in \Windows nor in \Programfiles\Pidgin\Data, however in PidginPortable the data file is by default stored in the same directory as the the launcher program.

Excerpt from Pidgin FAQ

Where are my settings and data (including logs) saved?
Where is my .purple directory?

Data is stored in your user's "Application Data" directory in a .purple subdirectory. The location of this will vary according to your setup and version of Windows.

    * For Windows 2000/XP/Vista/7, entering %APPDATA% in your Windows Explorer address bar will take you to the right directory
          o On Windows XP, it will be something like C:\Documents and Settings\username\Application Data.
          o On Windows Vista/7, it will be something like C:\Users\username\AppData\Roaming\. 
    * For Windows 98/ME it will be something like C:\Windows\Profiles\username. 

This can be overridden by setting the PURPLEHOME environment variable.

You can add/set the PURPLEHOME environment variable for your system in Start > Settings > Control Panel > System > Advanced > Environment Variables. 

Per the excerpt above it stores it by default in more modern OSes in a user data location or "your user's "Application Data" directory".
You can also see that with the "PURPLEHOME environment variable" you can change the data storage location.
This is probably how you are doing it in the PA pidgin launcher.
This feature should not be removed or fixed to a set unchangeable location even if is is a fixed relative position.
According to what you said you already removed the ability to support this when using the Pidgin launcher, and will be doing the same to other apps as they are updated.
Portable apps should be about being more flexible, not less.

The applications are equivalent to tools and are very important but are still very replaceable or re-installable.
Data is not, to reinstall and re-customize all the apps after accidentally deleting all 5 copies (separate devices) of the Apps folder would take a day or less. To recreate the Data may not be possible or could takes years, maybe a lifetime.

Data and application (tool) storage should be separated.
I don't store:
-mail under the mail box or with the letter opener.
-receipts with the stapler.
-notes and letters with the pens or pencils
-finished paintings with the brushes.
-bills with the checkbook.
-woodcarvings with the knives
-food in the utensils drawer, or pots or pans cupboard
-plumbing tools in the bathtub
-finished novels in the typewriter case.

Or at least I try not to as it make quite a mess.

I do file receipts, notes bills in a central data storage location, OK it is a filing cabinet.
I might put a painting or piece of art in a vault or on display.
Tools go in the toolbox in the garage or in specific location in the desk.

The tools (applications) are stored separate from the product (data).
When a tool is used "or an application is opened" it goes to where the "thing the tool is for" is "or where the data is stored". The toilet is not stored in the tool shed because the wrenches are there.

When someone mixes this all up it becomes a problem and things get lost.

What is required to maintain the data portability and flexibility in future PA.c applications so data and profile storage can be centralized and/or customized?

Jestre

Pyromaniac,
Do you keep your desktop background in the default location for those things or do you link to the current location of the picture you want to use (stored in your "Data" location where ever that is).
RE: "the launcher" I was intermixing a little the only reference to the PortableApps menu launcher was in reference to the backup, the rest were to application launchers.
Jestre

Darkbee,
I can commiserate for I to had lost data and configurations over the years and had to restore application customizations from scratch and rebuild complex index files that unruly applications chose to store hidden away in "ProgramFiles" instead of with the project file it was for.
Since adopting this structure and making the application store in a central location I have not had any significant data loss even with several hard drive failures and 2 systems that died.
This includes many of the "configuration" files to customize an app.
My custom configured profiles, themes and backgrounds were available since they were stored in the "data" location which is very backed up.
I am sorry to hear that you gave up on a environment suited to your needs, I will keep up the fight.
Jestre