I love the updating functionality of the suite, it's the main reason I use it. However there are some applications I don't wish updated, newer isn't always better. VLC2 requires .net, portable browser versions kept for web testing, and others.
It'd be great if there were an update exclusions list or something that resided in the suite's folder, or depending on how the update system works, perhaps a flag in the individual app's ini (AppnamePortable.ini) files.
It's indeed possible to just put apps you wish not to update in a different location, but the way I have everything set up, with a launcher and usb syncing and network syncing etc, it'd be a huge pain. I think it'd be a great option to add, and I'm sure some would appreciate it as much as I would.