Application that allows any program to become a portable app.

Might be.

I would suggest a system that makes a "portable registry" and that auto-compresses files. IDK if the Portable Registry is even possible, but it might work. I've seen a few batch files out there that seem to do the job; here's one:

http://osx.soc.uh.edu/~jdavis/blog/2005/12/making-applications-portable-...
@echo off
if not exist j_pmail.reg goto end
if exist %windir%\system32\reg.exe (set regapp=%windir%\system32\reg.exe) else (set regapp=reg.exe)
%regapp% export "HKCU\Software\Pegasus Mail" pmail-original.reg
%regapp% delete "HKCU\Software\Pegasus Mail" /f
%regapp% import j_pmail.reg
start /max /wait winpm-32.exe
%regapp% export "HKCU\Software\Pegasus Mail" pmail.reg
%regapp% delete "HKCU\Software\Pegasus Mail" /f
if exist pmail-original.reg %regapp% import pmail-original.reg
del pmail-original.reg >nul
set regapp=
:end
echo Done.

This is for an app called Pegasus Mail. You can get the basic idea and change it from there. Look and see what Registry entries are made, then back them up into Settings_AppName.reg. Then adjust this.

I'll post a modified version of this later, if I have time. It'll let you modify variables at the top of the code, instead of messing with everything. It shouldn't be too hard to port something like this to NSIS (I think JH already has a plan like this in the works), so somebody who can code in NSIS (http://nsis.sf.net) could work on this.

Cheers!
--nm35

Skype is very easy, just copy Skype.exe on your key and launch it using the parameters:

/datapath:"directory where skype data file are located" /removable

I use to put skype.exe in the public part of the usb key and I point it to use a directory in the encrypted disk I have on the usb (I use truecrypt to mount the crypted file as a virtual disk where I put all my personal data).