I've noticed this: some programs that apear to work portably, actually leave behind files in: C:\Documents and Settings\*User Directory*\Application Data (it's a hidden file) and in other places. When developing apps, it would probably be best to make sure your application doesn't do that.
Programs that do this:
uTorrent
Inkscape
Notepad++
USBOpera (I think so, but then again, since the physical folder is called "Opera" perhaps only the install version of Opera does this.)
Thankfully it only does this to the folder of the user you are logged in as.
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they can be beaten. For Utorrent, you just need to create a blank file called settings.dat in the application's folder and from then on it will save the settings to the application's folder.
As for Notepad++ you just need to tell not to save history under the settings menu. This will stop it from making anything on the host machine.
As for Inkscape and USBOpera, I don't use these, but maybe someone else can help.
I used these two programs daily on many pcs and have yet to leave traces.
Hopes this helps.
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Deuce {The Core}
"Portable Software: Just the beginning..."
Deuce
Portable Software: Just the beginning.